SMTL ID : 4ub8.2 (1 other biounit)

Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

7 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 3 residues within 4Å: Chain A: L.72, Y.73 Chain D: R.294 7 PLIP interactions: 1 interactions with chain M, 4 interactions with chain A, 2 interactions with chain D Water bridges: M:G.110, A:S.68, A:L.72 Hydrophobic interactions: A:L.72 Hydrogen bonds: A:Y.73, D:R.294, D:R.294 LMT.17: 9 residues within 4Å: Chain A: N.12, W.14, E.15 Chain C: W.241, R.244 Chain H: L.24, S.25, G.26, R.30 9 PLIP interactions: 3 interactions with chain H, 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: H:R.30, C:R.244, C:R.244, A:N.12, A:E.15 Water bridges: H:S.25, H:R.30 Hydrophobic interactions: C:W.241, C:W.241 LMT.20: 3 residues within 4Å: Chain B: Y.39, A.42 Ligands: LMT.112 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.39 LMT.44: 11 residues within 4Å: Chain B: R.223, L.224, K.226, K.497 Chain D: F.5, D.6 Chain G: W.24, A.31, M.34 Ligands: HTG.90, UNL.92 8 PLIP interactions: 2 interactions with chain D, 2 interactions with chain G, 4 interactions with chain B Hydrophobic interactions: D:F.5, G:W.24, G:A.31 Hydrogen bonds: D:D.6, B:R.223, B:K.226 Salt bridges: B:R.223, B:K.226 LMT.96: 6 residues within 4Å: Chain E: W.35, S.39 Chain F: F.41, I.42, Q.43 Chain I: V.22 4 PLIP interactions: 1 interactions with chain I, 2 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: I:V.22, E:W.35 Hydrogen bonds: F:Q.43, F:Q.43 LMT.111: 6 residues within 4Å: Chain L: V.27, E.30, S.31, Q.32, Q.33, K.34 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:V.27 Hydrogen bonds: L:E.30, L:Q.32, L:Q.33, L:K.34 LMT.112: 8 residues within 4Å: Chain B: Y.39 Chain L: N.4, Q.5, L.6 Ligands: LMT.20, CLA.37, LMG.43, GOL.48 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain L Water bridges: B:K.331, L:N.4, L:Q.5 Hydrogen bonds: L:Q.5

5 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.2: 14 residues within 4Å: Chain A: W.20, N.26, R.27, L.28, V.30, I.38, T.45 Chain N: F.22 Ligands: PHO.8, BCR.10, UNL.14, CLA.80, UNL.101, BCR.114 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.26, A:V.30, A:I.38, A:I.38 Hydrogen bonds: A:N.26, A:L.28 Water bridges: A:R.27, A:R.27 SQD.11: 23 residues within 4Å: Chain A: L.200, A.203, G.204, F.265, N.267, S.270, F.273, F.274, A.277, W.278, V.281, G.282 Chain C: Q.10, A.16, W.17, W.18 Chain D: F.222, R.223 Chain J: A.25, F.28 Ligands: CLA.62, LHG.89, UNL.105 22 PLIP interactions: 13 interactions with chain A, 3 interactions with chain C, 3 interactions with chain J, 3 interactions with chain D Hydrophobic interactions: A:L.200, A:A.203, A:F.265, A:F.274, A:A.277, A:W.278, A:W.278, A:W.278, A:V.281, C:W.17, C:W.18, J:A.25, J:F.28, J:F.28 Hydrogen bonds: A:N.267, A:S.270, C:Q.10 Water bridges: A:N.266, A:N.267, D:R.223, D:R.223 Salt bridges: D:R.223 SQD.19: 6 residues within 4Å: Chain B: R.17, S.103, W.114 Chain K: R.7 Ligands: CLA.37, BCR.40 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain K Water bridges: B:R.17, B:R.17, K:N.4 Salt bridges: B:R.17, K:R.7 SQD.95: 16 residues within 4Å: Chain D: W.11, R.14, R.16 Chain F: P.13, I.14, F.15, T.16, V.17, V.20 Chain R: T.23, V.26, L.27, I.30, D.34 Ligands: PL9.16, DGD.86 6 PLIP interactions: 2 interactions with chain R, 2 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: R:L.27, R:I.30 Hydrogen bonds: F:F.15, F:V.17, D:R.14 Salt bridges: D:R.16 SQD.108: 11 residues within 4Å: Chain K: R.14, Y.18 Chain L: V.15, L.16, Y.26 Chain N: C.12, A.15, L.16, F.19, F.23 Ligands: UNL.110 10 PLIP interactions: 4 interactions with chain N, 3 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: N:A.15, N:L.16, N:F.19, L:V.15, L:L.16 Hydrogen bonds: N:F.23, L:Y.26, K:R.14, K:R.14 Salt bridges: K:R.14

1 x FE2: FE (II) ION(Non-covalent)

FE2.3: 5 residues within 4Å: Chain A: H.215, H.272 Chain D: H.204, H.258 Ligands: BCT.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:H.215, A:H.272, D:H.204, D:H.258

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: N.181, H.332, E.333 Chain D: K.307 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: H.337, N.338, F.339 Chain C: G.335, E.336 Ligand excluded by PLIP CL.116: 1 residues within 4Å: Chain O: K.104 Ligand excluded by PLIP

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.6: 29 residues within 4Å: Chain A: F.119, Y.147, P.150, L.151, S.153, V.157, F.182, M.183, F.186, Q.187, I.192, L.193, H.198, G.201, V.202, V.205, F.206, V.283, A.286, A.287, I.290 Chain D: L.172, L.195 Chain N: F.17 Ligands: CLA.7, PHO.8, CLA.80, CLA.81, LHG.88 17 PLIP interactions: 14 interactions with chain A, 1 interactions with chain N, 2 interactions with chain D, Hydrophobic interactions: A:F.119, A:P.150, A:F.182, A:M.183, A:F.186, A:Q.187, A:I.192, A:I.192, A:L.193, A:V.205, A:F.206, A:F.206, A:I.290, N:F.17, D:L.172, D:L.195 Metal complexes: A:H.198 CLA.7: 19 residues within 4Å: Chain A: Q.199, V.202, A.203, F.206, G.207, L.210, F.211, W.278 Chain D: F.147, V.165, I.168, F.169, L.172 Ligands: CLA.6, PL9.16, DGD.71, CLA.81, PHO.82, LMG.102 14 PLIP interactions: 7 interactions with chain A, 6 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.202, A:V.202, A:F.206, A:L.210, A:F.211, A:W.278, D:F.147, D:F.147, D:I.168, D:F.169, D:L.172, D:L.172 pi-Stacking: A:F.206 Metal complexes: H2O.3 CLA.9: 28 residues within 4Å: Chain A: I.36, P.39, T.40, F.93, Y.94, P.95, I.96, W.97, Q.113, L.114, F.117, H.118, L.121 Chain H: V.8, Y.9, V.11, V.12, T.13, F.15, V.16, F.19 Ligands: BCR.10, LMG.53, CLA.59, CLA.60, BCR.68, DGD.69, UNL.101 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain H, Hydrophobic interactions: A:P.39, A:T.40, A:F.93, A:P.95, A:I.96, A:W.97, A:W.97, A:L.114, A:L.121, H:Y.9, H:V.11, H:F.15, H:F.15, H:V.16, H:F.19 Hydrogen bonds: A:I.96 Salt bridges: A:H.118 Metal complexes: A:H.118 CLA.24: 11 residues within 4Å: Chain B: W.184, G.185, P.186, F.189, V.207 Chain G: F.33, F.40, L.54 Ligands: CLA.25, HTG.46, BCR.99 11 PLIP interactions: 6 interactions with chain B, 4 interactions with chain G, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.184, B:P.186, B:F.189, B:F.189, B:F.189, B:V.207, G:F.33, G:F.40, G:F.40, G:L.54 Metal complexes: H2O.10 CLA.25: 26 residues within 4Å: Chain B: W.184, G.188, F.189, P.191, G.196, A.199, H.200, A.203, A.204, V.207, F.245, F.246, F.249, V.250 Chain D: L.148 Chain G: F.37, F.40, I.44, L.45, Y.48 Ligands: CLA.24, CLA.26, CLA.28, CLA.32, BCR.99, DGD.100 19 PLIP interactions: 13 interactions with chain B, 5 interactions with chain G, 1 interactions with chain D, Hydrophobic interactions: B:W.184, B:F.189, B:F.189, B:F.189, B:A.199, B:H.200, B:A.204, B:V.207, B:F.245, B:F.246, B:F.246, B:F.249, G:F.37, G:I.44, G:I.44, G:Y.48, D:L.148 Metal complexes: B:H.200 pi-Stacking: G:F.40 CLA.26: 24 residues within 4Å: Chain B: R.67, L.68, A.145, L.148, C.149, F.152, M.165, H.200, H.201, F.246, A.247, V.250, V.251, T.261 Chain G: M.34, F.37, L.41 Ligands: CLA.25, CLA.27, CLA.28, CLA.29, CLA.31, CLA.32, CLA.33 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: B:L.68, B:A.145, B:L.148, B:F.152, B:F.152, B:F.152, B:F.246, B:F.246, B:A.247, B:V.251, G:F.37 Hydrogen bonds: B:R.67 Salt bridges: B:R.67 pi-Cation interactions: B:H.200 Metal complexes: B:H.201 CLA.27: 24 residues within 4Å: Chain B: W.32, F.60, F.64, R.67, L.144, L.147, L.148, V.244, A.247, A.248, V.251, F.450, H.454, F.457, A.458, F.461 Ligands: CLA.26, CLA.28, CLA.30, CLA.34, CLA.35, CLA.36, CLA.38, BCR.41 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.32, B:F.60, B:F.60, B:F.64, B:L.147, B:L.148, B:V.244, B:A.247, B:F.457, B:F.457, B:F.457, B:F.461, B:F.461 Salt bridges: B:R.67 Metal complexes: B:H.454 CLA.28: 29 residues within 4Å: Chain B: T.26, V.29, A.30, W.32, A.33, A.37, V.61, F.64, M.65, R.67, L.68, V.95, H.99, L.102, L.142, A.145, G.146, C.149, A.204, G.208 Ligands: CLA.25, CLA.26, CLA.27, CLA.29, CLA.33, CLA.35, CLA.38, BCR.42, UNL.52 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:V.29, B:W.32, B:A.33, B:L.68, B:V.95, B:L.102, B:L.142, B:A.145 Water bridges: B:R.67 Salt bridges: B:R.67 Metal complexes: B:H.99 CLA.29: 23 residues within 4Å: Chain B: L.68, G.69, V.70, F.89, W.90, V.95, A.98, H.99, V.101, L.102, L.148, G.151, F.152, F.155, H.156, F.161, G.162, P.163 Ligands: HTG.22, CLA.26, CLA.28, BCR.42, UNL.52 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:L.68, B:V.70, B:F.89, B:F.89, B:F.89, B:W.90, B:W.90, B:W.90, B:A.98, B:V.101, B:L.102, B:L.148, B:L.148, B:F.155, B:F.161, B:F.161 Metal complexes: B:H.156 CLA.30: 27 residues within 4Å: Chain B: W.32, M.36, Y.39, Q.57, G.58, M.59, F.60, L.323, F.324, T.326, G.327, P.328, W.449, F.450, A.453 Chain D: F.186, T.267, M.271 Chain K: F.31 Chain L: F.14 Ligands: CLA.27, CLA.36, BCR.40, BCR.41, LMG.43, PL9.85, LHG.87 14 PLIP interactions: 9 interactions with chain B, 2 interactions with chain D, 1 interactions with chain L, 1 interactions with chain K, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.39, B:F.60, B:F.324, B:W.449, B:W.449, B:W.449, B:A.453, D:F.186, D:T.267, L:F.14, K:F.31 Hydrogen bonds: B:G.327 pi-Stacking: B:F.60 Metal complexes: H2O.9 CLA.31: 22 residues within 4Å: Chain B: L.228, T.235, S.238, S.239, A.242, F.245, F.462, H.465, I.466, G.469, T.472, L.473 Chain D: F.110, I.113, M.116, L.117, F.120 Ligands: CLA.26, CLA.32, CLA.33, CLA.83, UNL.92 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain D, Hydrophobic interactions: B:A.242, B:F.245, B:F.462, B:F.462, B:I.466, B:L.473, D:F.110, D:F.110, D:F.110, D:I.113, D:M.116, D:L.117, D:L.117, D:F.120 Hydrogen bonds: B:S.238 Metal complexes: B:H.465 CLA.32: 25 residues within 4Å: Chain B: F.138, L.142, V.207, A.211, F.214, H.215, V.218, R.219, P.220, P.221, L.224, L.228 Chain G: T.26, T.27, L.29, M.30, F.33, M.34, L.42 Ligands: CLA.25, CLA.26, CLA.31, CLA.33, UNL.92, BCR.99 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain G, Hydrophobic interactions: B:F.138, B:F.138, B:L.142, B:V.207, B:A.211, B:F.214, B:F.214, B:L.228, G:L.29, G:M.30, G:F.33 Salt bridges: B:H.215 Metal complexes: B:H.215 CLA.33: 19 residues within 4Å: Chain B: L.134, M.137, F.138, H.141, L.142, A.145, M.230, T.235, V.236, S.239, S.240, A.243 Ligands: CLA.26, CLA.28, CLA.31, CLA.32, CLA.35, CLA.38, BCR.99 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.134, B:M.137, B:F.138, B:M.230, B:T.235 Hydrogen bonds: B:H.141 Metal complexes: H2O.9 CLA.34: 23 residues within 4Å: Chain B: W.4, Y.5, R.6, V.7, H.8, T.9, L.237, I.241, F.457, L.460, F.461, F.463, G.464, W.467, H.468, R.471 Chain L: F.21 Ligands: CLA.27, CLA.35, CLA.36, CLA.37, LHG.87, LHG.109 16 PLIP interactions: 1 interactions with chain L, 15 interactions with chain B, Hydrophobic interactions: L:F.21, B:W.4, B:W.4, B:H.8, B:L.237, B:L.237, B:I.241, B:F.457, B:F.461, B:F.463, B:F.463 Hydrogen bonds: B:H.8 Salt bridges: B:H.8, B:R.471 pi-Stacking: B:W.467 Metal complexes: B:H.468 CLA.35: 21 residues within 4Å: Chain B: H.8, L.11, I.12, L.18, A.21, H.22, H.25, T.26, I.233, V.236, L.237, S.240, I.241, V.244 Ligands: CLA.27, CLA.28, CLA.33, CLA.34, CLA.36, CLA.37, CLA.38 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:H.8, B:L.11, B:I.12, B:L.18, B:A.21, B:H.22, B:H.25, B:T.26, B:I.233, B:V.236, B:L.237, B:L.237, B:V.244 Hydrogen bonds: B:S.240 Salt bridges: B:H.22 Metal complexes: B:H.22 CLA.36: 14 residues within 4Å: Chain B: H.8, H.25, V.29, W.32, F.461 Ligands: CLA.27, CLA.30, CLA.34, CLA.35, CLA.37, BCR.40, BCR.41, LMG.43, LHG.87 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:V.29, B:V.29, B:W.32, B:W.32, B:F.461, B:F.461, B:F.461 Salt bridges: B:H.8 Metal complexes: B:H.25 CLA.37: 19 residues within 4Å: Chain B: V.7, H.8, V.10, L.11, A.21, M.24, L.28, W.114 Chain K: Q.8, V.10 Chain L: F.21, L.25 Ligands: SQD.19, CLA.34, CLA.35, CLA.36, BCR.40, LHG.109, LMT.112 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain L, Hydrophobic interactions: B:V.7, B:V.7, B:L.11, B:M.24, B:L.28, B:W.114, L:F.21, L:L.25 Metal complexes: B:H.8 CLA.38: 19 residues within 4Å: Chain B: I.19, H.22, L.23, T.26, L.132, M.137, I.140, H.141, L.144 Chain G: L.6, L.10, L.13, N.14 Ligands: CLA.27, CLA.28, CLA.33, CLA.35, CLA.39, BCR.42 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain G, Hydrophobic interactions: B:I.19, B:L.132, B:L.144, G:L.6, G:L.10, G:L.13, G:L.13, G:N.14 Hydrogen bonds: B:H.22 Metal complexes: B:H.141 CLA.39: 13 residues within 4Å: Chain B: I.19, L.23, A.109, W.112, H.113, L.119, F.122 Chain G: T.4, L.6, G.7, L.10 Ligands: CLA.38, BCR.42 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain G, Hydrophobic interactions: B:I.19, B:I.19, B:L.23, B:A.109, B:W.112, B:W.112, B:L.119, B:F.122, G:L.6, G:L.10 pi-Stacking: B:W.112, B:W.112 Metal complexes: B:H.113 Hydrogen bonds: G:T.4 Water bridges: G:L.6 CLA.55: 22 residues within 4Å: Chain C: T.76, L.77, L.150, G.153, A.154, L.157, L.167, I.206, V.215, H.219, I.222, A.260, M.264, I.267, F.271, V.278, Y.279 Ligands: CLA.56, CLA.57, CLA.60, CLA.61, BCR.68 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.157, C:I.206, C:I.222, C:I.222, C:A.260, C:M.264, C:I.267, C:F.271, C:V.278 Hydrogen bonds: C:Y.279 Metal complexes: C:H.219 CLA.56: 22 residues within 4Å: Chain C: W.45, I.69, H.73, L.77, L.156, F.164, L.261, M.264, A.268, V.272, Y.279, L.408, H.412, L.415, A.416, F.419 Ligands: CLA.55, CLA.57, CLA.58, CLA.64, CLA.66, HTG.74 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:W.45, C:W.45, C:I.69, C:L.77, C:L.156, C:F.164, C:L.261, C:M.264, C:A.268, C:L.408, C:L.415, C:L.415, C:F.419 Hydrogen bonds: C:Y.279 Salt bridges: C:H.73, C:H.412 Metal complexes: C:H.412 CLA.57: 18 residues within 4Å: Chain C: I.42, V.43, A.46, T.50, L.70, H.73, I.74, L.77, V.96, H.100 Ligands: CLA.55, CLA.56, CLA.61, CLA.63, CLA.64, CLA.66, CLA.67, LMG.73 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:V.43, C:A.46, C:L.77, C:V.96 Salt bridges: C:H.73 Metal complexes: C:H.100 CLA.58: 19 residues within 4Å: Chain C: W.45, M.49, F.52, Q.66, G.67, I.69, W.407, S.411, H.412, F.418 Chain J: P.17, V.21 Ligands: CLA.56, CLA.62, CLA.64, DGD.70, DGD.71, LMG.72, LHG.89 8 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: C:W.45, C:F.52, C:I.69, C:W.407, C:W.407, C:F.418, J:V.21 Metal complexes: H2O.21 CLA.59: 23 residues within 4Å: Chain A: F.33, L.121, S.124, C.125, G.128, W.131 Chain C: F.246, S.255, Y.256, G.259, A.260, M.263, L.420, H.423, L.424, A.427, R.431 Chain H: V.16, F.23 Ligands: CLA.9, LMG.53, CLA.61, BCR.68 18 PLIP interactions: 9 interactions with chain C, 7 interactions with chain A, 2 interactions with chain H, Hydrophobic interactions: C:F.246, C:Y.256, C:Y.256, C:L.420, A:F.33, A:F.33, A:L.121, A:W.131, A:W.131, A:W.131, H:V.16, H:F.23 Hydrogen bonds: C:Y.256 Water bridges: C:I.247, C:I.247 Salt bridges: C:R.431 Metal complexes: C:H.423 pi-Stacking: A:W.131 CLA.60: 19 residues within 4Å: Chain C: L.143, L.147, L.195, I.225, G.229, W.232, H.233, T.236, T.237, P.238, F.239, W.241, A.242, F.246 Ligands: CLA.9, LMG.53, CLA.55, CLA.61, BCR.68 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:L.147, C:L.147, C:L.195, C:W.232, C:W.241, C:F.246 Hydrogen bonds: C:F.239 Salt bridges: C:H.233 Metal complexes: C:H.233 CLA.61: 21 residues within 4Å: Chain C: M.139, T.140, L.143, H.146, L.147, L.150, C.226, F.246, W.248, Y.253, Y.256, S.257, A.260, L.261, M.264 Ligands: CLA.55, CLA.57, CLA.59, CLA.60, CLA.63, BCR.68 13 PLIP interactions: 12 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:M.139, C:T.140, C:L.143, C:L.150, C:F.246, C:F.246, C:W.248, C:Y.253, C:Y.253, C:Y.256, C:Y.256, C:L.261 Metal complexes: H2O.20 CLA.62: 24 residues within 4Å: Chain C: F.15, W.18, A.19, G.20, N.21, A.22, E.251, L.254, L.258, F.418, F.419, G.422, W.425, H.426, R.429 Ligands: SQD.11, CLA.58, CLA.63, CLA.64, CLA.65, DGD.70, DGD.71, LMG.72, LHG.89 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:A.19, C:L.254, C:L.254, C:L.258, C:F.419, C:W.425 Hydrogen bonds: C:N.21, C:N.21 Salt bridges: C:H.426, C:R.429 pi-Stacking: C:W.425 Metal complexes: C:H.426 CLA.63: 23 residues within 4Å: Chain C: N.21, L.24, I.25, L.31, A.34, H.35, H.38, Y.131, W.133, H.146, L.150, G.250, E.251, Y.253, L.254, S.257, L.258 Ligands: CLA.57, CLA.61, CLA.62, CLA.64, CLA.65, CLA.66 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:N.21, C:L.24, C:A.34, C:H.38, C:Y.131, C:W.133, C:W.133, C:L.150, C:Y.253 Hydrogen bonds: C:S.257 Metal complexes: C:H.35 CLA.64: 18 residues within 4Å: Chain C: N.21, H.38, L.41, I.42, W.45, L.261, F.418, F.419 Chain J: P.20, V.21, L.24 Ligands: CLA.56, CLA.57, CLA.58, CLA.62, CLA.63, CLA.65, LHG.89 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain J, Hydrophobic interactions: C:L.41, C:I.42, C:W.45, C:L.261, C:F.418, C:F.419, J:P.20, J:V.21, J:L.24 Hydrogen bonds: C:N.21 Metal complexes: C:H.38 CLA.65: 31 residues within 4Å: Chain C: R.8, W.17, G.20, N.21, R.23, L.24, L.27, K.30, A.34, L.41, F.109, V.112, I.116 Chain J: F.23, L.24, A.27, W.30, Q.31 Chain Q: L.23, N.29, L.30 Chain S: M.19, V.20, V.23, P.24, A.28 Ligands: CLA.62, CLA.63, CLA.64, BCR.107, LMG.124 19 PLIP interactions: 8 interactions with chain J, 1 interactions with chain Q, 5 interactions with chain C, 5 interactions with chain S, Hydrophobic interactions: J:F.23, J:F.23, J:L.24, J:A.27, J:W.30, J:Q.31, Q:L.30, C:L.24, C:L.24, C:L.41, S:M.19, S:V.20, S:V.23, S:P.24, S:A.28 pi-Stacking: J:W.30, J:W.30 Hydrogen bonds: C:R.23 Salt bridges: C:R.8 CLA.66: 19 residues within 4Å: Chain C: L.32, H.35, A.39, L.107, F.128, F.129, Y.131, I.142, F.145, H.146, I.148, V.149, I.152, G.153 Ligands: CLA.56, CLA.57, CLA.63, CLA.67, BCR.78 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.32, C:H.35, C:F.128, C:Y.131, C:I.142, C:F.145, C:I.148, C:V.149, C:I.152, C:I.152 Metal complexes: C:H.146 CLA.67: 14 residues within 4Å: Chain C: L.32, V.36, V.106, G.110, Y.113, H.114, P.119, Y.125, F.129 Ligands: CLA.57, CLA.66, LMG.73, BCR.78, LMG.124 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.32, C:L.32, C:V.36, C:V.106, C:Y.113, C:Y.125, C:F.129, C:F.129 Hydrogen bonds: C:Y.113 pi-Stacking: C:F.129 Metal complexes: C:H.114 CLA.80: 23 residues within 4Å: Chain A: T.45, F.48, V.157, F.158, M.172, I.176, T.179, F.180, F.182, M.183 Chain D: M.188, V.191, A.192, L.195, G.196, L.199 Ligands: SQD.2, CLA.6, PHO.8, CLA.81, PL9.85, LHG.88, LHG.109 7 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.48, A:V.157, A:F.158, A:F.180, A:F.182, D:V.191 Metal complexes: H2O.3 CLA.81: 30 residues within 4Å: Chain A: M.183, F.206 Chain D: L.35, W.38, L.112, P.139, V.142, F.143, S.145, V.146, F.171, L.172, F.175, Q.176, W.181, T.182, H.187, G.190, V.191, V.194, L.195, L.269, S.272, A.273, V.276 Ligands: CLA.6, CLA.7, PL9.16, CLA.80, PHO.82 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:L.35, D:W.38, D:L.112, D:V.142, D:F.143, D:F.171, D:F.175, D:Q.176, D:W.181, D:T.182, D:V.191, D:V.194, D:V.194, D:L.195, D:L.269 pi-Stacking: D:W.181 Metal complexes: D:H.187 CLA.83: 29 residues within 4Å: Chain D: I.25, L.26, P.29, C.30, L.33, L.79, L.80, L.81, L.82, W.83, W.94, T.102, F.103, L.106, H.107 Chain G: V.32, G.35, L.38, V.39, L.42 Chain R: G.12, L.13, G.16, A.17, V.19 Ligands: CLA.31, DGD.86, UNL.91, UNL.123 15 PLIP interactions: 11 interactions with chain D, 1 interactions with chain R, 3 interactions with chain G, Hydrophobic interactions: D:L.26, D:P.29, D:L.33, D:L.82, D:W.83, D:W.83, D:L.106, R:V.19, G:V.32, G:L.38, G:V.39 Hydrogen bonds: D:L.82 Salt bridges: D:H.107 pi-Stacking: D:F.103 Metal complexes: D:H.107

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.8: 30 residues within 4Å: Chain A: L.41, A.44, T.45, F.48, I.115, F.119, Y.126, Q.130, A.146, Y.147, P.150, F.158, M.172, G.175, T.179, V.205, P.279, V.283 Chain D: L.195, A.198, L.199, A.202, I.203, W.243, F.247 Ligands: SQD.2, CLA.6, CLA.80, PL9.85, LHG.88 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:L.41, A:A.44, A:F.48, A:I.115, A:F.119, A:A.146, A:Y.147, A:P.150, A:F.158, A:V.205, A:V.283, D:L.195, D:A.198, D:A.202 Hydrogen bonds: A:Q.130, A:Y.147 pi-Stacking: A:Y.147 PHO.82: 32 residues within 4Å: Chain A: F.206, A.209, L.210, M.214, F.255, L.258, I.259 Chain D: L.27, A.31, A.34, L.35, W.38, I.104, G.108, G.111, L.112, F.115, Q.119, N.132, A.135, F.136, A.138, P.139, F.143, G.164, V.165, P.265, V.266, L.269 Ligands: CLA.7, PL9.16, CLA.81 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.31, D:A.34, D:W.38, D:W.38, D:W.38, D:W.38, D:I.104, D:L.112, D:F.115, D:F.115, D:A.135, D:A.138, D:P.139, D:F.143, D:V.165, D:P.265, D:V.266, D:L.269, D:L.269, A:F.206 Hydrogen bonds: D:N.132 pi-Stacking: D:F.136, D:F.136

11 x BCR: BETA-CAROTENE(Non-covalent)

BCR.10: 16 residues within 4Å: Chain A: V.35, I.38, L.42, A.43, I.46, I.50, A.51, A.55, I.96, W.105, L.106 Chain H: F.15 Ligands: SQD.2, CLA.9, UNL.14, UNL.101 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:V.35, A:I.38, A:L.42, A:A.43, A:I.46, A:I.50, A:A.51, A:I.96, A:W.105, A:W.105, A:L.106, H:F.15 BCR.40: 12 residues within 4Å: Chain B: M.24, L.28, C.111, W.114 Chain L: L.6, A.10 Ligands: SQD.19, CLA.30, CLA.36, CLA.37, BCR.41, LMG.43 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain L Hydrophobic interactions: B:L.28, B:L.28, B:W.114, B:W.114, L:L.6, L:A.10 BCR.41: 14 residues within 4Å: Chain B: L.28, G.31, W.32, S.35, I.100, V.101, S.103, G.104, L.108 Ligands: CLA.27, CLA.30, CLA.36, BCR.40, LMG.43 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.108 BCR.42: 11 residues within 4Å: Chain B: L.105, L.108, A.109, W.112, V.115, Y.116 Ligands: CLA.28, CLA.29, CLA.38, CLA.39, UNL.52 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.112, B:V.115, B:Y.116 BCR.68: 19 residues within 4Å: Chain C: I.191, F.192, Y.194, L.195, I.206, V.209, V.215, G.218, H.219, I.222, F.246 Chain H: V.20, F.23, L.24 Ligands: CLA.9, CLA.55, CLA.59, CLA.60, CLA.61 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: C:I.191, C:F.192, C:Y.194, C:L.195, C:L.195, C:I.206, C:V.209, C:I.222, C:I.222, C:F.246, H:F.23, H:L.24 BCR.78: 14 residues within 4Å: Chain C: F.94, V.98, I.102, S.103, V.106, F.129 Chain J: Y.6 Chain S: V.51, G.55, N.58, F.59 Ligands: CLA.66, CLA.67, LMG.73 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain S Hydrophobic interactions: C:F.94, C:V.98, C:I.102, C:V.106, C:F.129, S:F.59 BCR.84: 17 residues within 4Å: Chain D: Y.32, L.33, G.36, G.37, L.39, T.40, F.91, F.103 Chain F: P.28, T.29, F.32, L.33, I.36 Chain I: V.20, V.24 Ligands: DGD.86, LMG.102 15 PLIP interactions: 6 interactions with chain F, 2 interactions with chain I, 7 interactions with chain D Hydrophobic interactions: F:P.28, F:T.29, F:F.32, F:F.32, F:L.33, F:I.36, I:V.20, I:V.24, D:Y.32, D:L.39, D:L.39, D:L.39, D:F.91, D:F.103, D:F.103 BCR.99: 14 residues within 4Å: Chain G: M.30, F.33, M.34, L.36, F.37, V.39, F.40, I.43 Chain R: I.2, L.6 Ligands: CLA.24, CLA.25, CLA.32, CLA.33 9 PLIP interactions: 7 interactions with chain G, 2 interactions with chain R Hydrophobic interactions: G:F.37, G:F.37, G:F.37, G:F.37, G:V.39, G:F.40, G:I.43, R:I.2, R:L.6 BCR.107: 19 residues within 4Å: Chain C: A.37, G.40, L.41, F.44, L.51, L.101, S.104, A.105, G.108, A.115 Chain J: Y.6, F.23, L.26, W.30 Chain S: L.9, S.16 Ligands: CLA.65, BCR.122, LMG.124 14 PLIP interactions: 6 interactions with chain J, 7 interactions with chain C, 1 interactions with chain S Hydrophobic interactions: J:Y.6, J:Y.6, J:F.23, J:F.23, J:L.26, J:W.30, C:A.37, C:L.41, C:F.44, C:F.44, C:L.51, C:A.105, C:A.115, S:L.9 BCR.114: 12 residues within 4Å: Chain A: L.28 Chain N: I.4, F.8, A.11, C.12, I.14, A.15, F.17, F.18, I.21, F.22 Ligands: SQD.2 8 PLIP interactions: 7 interactions with chain N, 1 interactions with chain A Hydrophobic interactions: N:I.4, N:F.8, N:I.14, N:F.18, N:F.18, N:I.21, N:F.22, A:L.28 BCR.122: 21 residues within 4Å: Chain C: F.44 Chain I: A.13, T.14, G.17, M.18 Chain J: L.12, L.16, I.19, L.22, F.23, A.25, F.28, V.29 Chain Q: I.12, G.13, G.16, P.17 Chain S: V.13, S.16, F.17 Ligands: BCR.107 11 PLIP interactions: 9 interactions with chain J, 1 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: J:L.12, J:L.16, J:I.19, J:I.19, J:L.22, J:L.22, J:F.23, J:A.25, J:V.29, I:A.13, C:F.44

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 8 residues within 4Å: Chain A: G.74, N.75, N.76 Chain D: S.290, Q.291 Chain L: M.1 Chain N: E.2, Y.6 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: V.313, N.315 Chain D: W.48, G.52, Q.322 Chain E: Y.56, I.63 Chain P: K.129 Ligand excluded by PLIP GOL.47: 8 residues within 4Å: Chain B: W.274, D.275, S.277, R.356, R.357, M.358, P.359 Chain D: E.327 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain B: K.331, N.437, D.439, R.443 Chain D: I.289 Chain L: V.3 Ligands: LMT.112 Ligand excluded by PLIP GOL.49: 8 residues within 4Å: Chain B: R.384, A.385, E.386, S.387, Q.393 Chain O: L.17, Y.21, G.22 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain B: I.12, N.13, A.131, L.132, G.231, N.232, I.233 Ligand excluded by PLIP GOL.51: 7 residues within 4Å: Chain B: P.49, P.53, I.79, T.80, W.166, E.265, K.307 Ligand excluded by PLIP GOL.76: 10 residues within 4Å: Chain A: L.341, L.343 Chain C: M.378, T.379, H.380, A.381, G.391, V.392, E.395 Chain P: K.47 Ligand excluded by PLIP GOL.77: 6 residues within 4Å: Chain C: I.301, R.302, K.305, E.371 Chain P: N.49 Ligands: HEC.118 Ligand excluded by PLIP GOL.79: 6 residues within 4Å: Chain C: N.355 Chain M: I.8, L.13, K.16, P.18, R.40 Ligand excluded by PLIP GOL.98: 6 residues within 4Å: Chain A: A.309 Chain F: R.44 Chain P: L.3, E.23, L.27 Ligands: CA.97 Ligand excluded by PLIP GOL.115: 5 residues within 4Å: Chain D: S.252 Chain K: T.15 Chain N: E.25, P.27 Ligands: LHG.88 Ligand excluded by PLIP GOL.117: 6 residues within 4Å: Chain B: E.386 Chain O: A.33, Y.103, K.104 Chain P: P.50, S.51 Ligand excluded by PLIP GOL.119: 6 residues within 4Å: Chain P: S.14, P.64, P.65, N.68, E.70, G.71 Ligand excluded by PLIP GOL.120: 5 residues within 4Å: Chain P: P.11, N.13, S.14, D.67, N.68 Ligand excluded by PLIP GOL.121: 4 residues within 4Å: Chain O: K.104 Chain P: G.133, K.134, Y.137 Ligand excluded by PLIP

10 x UNL: UNKNOWN LIGAND

UNL.14: 7 residues within 4Å: Chain A: L.13, R.16, F.17, W.20 Ligands: SQD.2, BCR.10, UNL.101 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.13, A:W.20, A:W.20 Salt bridges: A:R.16 UNL.52: 5 residues within 4Å: Chain B: W.90 Ligands: HTG.22, CLA.28, CLA.29, BCR.42 No protein-ligand interaction detected (PLIP) UNL.91: 8 residues within 4Å: Chain D: W.22, S.23, F.120, E.121, R.124 Chain R: L.20 Ligands: CLA.83, UNL.92 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain D Hydrophobic interactions: R:L.20, D:E.121 UNL.92: 12 residues within 4Å: Chain B: A.227, L.228, L.473 Chain D: D.9, K.13, W.22 Chain G: L.38 Chain R: F.24 Ligands: CLA.31, CLA.32, LMT.44, UNL.91 9 PLIP interactions: 2 interactions with chain R, 2 interactions with chain B, 4 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: R:F.24, R:F.24, B:A.227, B:L.228, D:W.22, D:W.22, G:L.38 Hydrogen bonds: D:K.13 Salt bridges: D:K.13 UNL.101: 10 residues within 4Å: Chain A: A.100 Chain H: M.1, E.2, T.3, L.4, T.7 Ligands: SQD.2, CLA.9, BCR.10, UNL.14 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:L.4, H:L.4, H:T.7 Hydrogen bonds: H:E.2, H:T.3 Water bridges: A:A.99 UNL.104: 3 residues within 4Å: Chain I: G.25 Ligands: DGD.70, LMG.72 No protein-ligand interaction detected (PLIP) UNL.105: 4 residues within 4Å: Chain C: W.17 Chain J: F.36 Ligands: SQD.11, LHG.89 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:F.36, J:F.36, J:F.36 UNL.106: 4 residues within 4Å: Chain I: L.9 Chain J: A.32, G.35, F.36 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:L.9, J:F.36 UNL.110: 2 residues within 4Å: Chain L: I.23 Ligands: SQD.108 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:I.23, L:I.23 UNL.123: 5 residues within 4Å: Chain D: W.83 Chain R: S.15, G.16, V.19 Ligands: CLA.83 1 PLIP interactions: 1 interactions with chain R Hydrophobic interactions: R:V.19

1 x OEX: CA-MN4-O5 CLUSTER(Covalent)

OEX.15: 10 residues within 4Å: Chain A: D.170, V.185, E.189, H.332, E.333, H.337, D.342, A.344 Chain C: E.336, R.339 19 PLIP interactions: 11 interactions with chain A, 4 interactions with chain C, 4 Ligand-Water interactions Water bridges: A:D.61 Metal complexes: A:D.170, A:D.170, A:E.189, A:H.332, A:E.333, A:E.333, A:D.342, A:D.342, A:A.344, A:A.344, C:E.336, C:E.336, H2O.1, H2O.1, H2O.3, H2O.3 Hydrogen bonds: C:R.339, C:R.339

2 x PL9: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE(Non-covalent)

PL9.16: 29 residues within 4Å: Chain A: F.211, M.214, H.215, L.218, A.251, H.252, F.255, I.259, A.263, S.264, F.265, L.271, F.274 Chain D: V.20, G.24, F.28, P.29, Y.32, L.35 Chain F: A.21, T.24, L.25 Chain R: T.23, L.27 Ligands: CLA.7, CLA.81, PHO.82, LHG.93, SQD.95 23 PLIP interactions: 15 interactions with chain A, 5 interactions with chain D, 2 interactions with chain R, 1 interactions with chain F Hydrophobic interactions: A:F.211, A:F.211, A:H.215, A:L.218, A:A.251, A:H.252, A:F.255, A:F.255, A:I.259, A:I.259, A:F.265, A:L.271, A:L.271, A:F.274, D:V.20, D:P.29, D:Y.32, D:Y.32, D:L.35, R:T.23, R:L.27, F:L.25 Hydrogen bonds: A:F.265 PL9.85: 32 residues within 4Å: Chain A: F.52, I.53, I.77 Chain D: M.188, M.189, A.192, G.193, L.199, I.203, H.204, T.207, M.236, A.239, N.240, W.243, I.249, A.250, F.251, L.257, F.260, F.263, V.264, G.268 Chain K: L.23, V.26, L.29 Chain N: F.10 Ligands: PHO.8, CLA.30, CLA.80, LHG.88, LHG.109 28 PLIP interactions: 3 interactions with chain K, 17 interactions with chain D, 4 interactions with chain N, 4 interactions with chain A Hydrophobic interactions: K:L.23, K:V.26, K:L.29, D:M.188, D:M.189, D:A.192, D:L.199, D:I.203, D:T.207, D:W.243, D:F.251, D:F.251, D:L.257, D:F.260, D:F.263, D:V.264, N:F.10, N:F.10, N:F.10, N:F.10, A:F.52, A:F.52, A:I.53, A:I.77 Hydrogen bonds: D:H.204, D:T.207, D:F.251 pi-Stacking: D:F.251

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.18: 9 residues within 4Å: Chain A: H.215, V.219, E.244, Y.246, H.272 Chain D: H.204, Y.234, H.258 Ligands: FE2.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.215, A:E.244

7 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)

HTG.21: 6 residues within 4Å: Chain B: W.74, D.86, G.88, F.89, L.97 Ligands: HTG.22 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.97 Hydrogen bonds: B:D.86, B:D.86, B:G.88, B:G.88 HTG.22: 6 residues within 4Å: Chain B: D.86, G.88, F.89 Ligands: HTG.21, CLA.29, UNL.52 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.89, B:F.89 Hydrogen bonds: B:D.86, B:F.89 Water bridges: B:W.90 HTG.45: 12 residues within 4Å: Chain B: K.340, Y.419, K.422, F.429, E.430, F.431, T.433 Chain M: Q.174, A.175, K.176, E.177, E.178 10 PLIP interactions: 4 interactions with chain M, 6 interactions with chain B Hydrophobic interactions: M:E.178, B:Y.419 Hydrogen bonds: M:Q.174, M:K.176, B:K.340, B:K.340, B:K.422, B:F.431, B:F.431 Water bridges: M:E.177 HTG.46: 4 residues within 4Å: Chain B: W.184, I.206, V.207 Ligands: CLA.24 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.184, B:I.206, B:I.206, B:V.207 HTG.74: 4 residues within 4Å: Chain C: W.79, F.164, G.165 Ligands: CLA.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.79 HTG.75: 6 residues within 4Å: Chain C: V.158, F.163, N.183, P.184, L.186, I.220 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.158, C:F.163 Hydrogen bonds: C:N.183, C:N.183 HTG.90: 6 residues within 4Å: Chain D: G.3, W.4, F.5 Chain G: W.24, P.28 Ligands: LMT.44 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.5 Hydrogen bonds: D:G.3, D:F.5

4 x CA: CALCIUM ION(Non-covalent)

CA.23: 1 residues within 4Å: Chain B: N.437 No protein-ligand interaction detected (PLIP) CA.54: 5 residues within 4Å: Chain C: F.4, T.6, D.9, E.11, S.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:F.4, C:T.6, C:E.11, C:S.12, H2O.22 CA.97: 2 residues within 4Å: Chain F: R.44 Ligands: GOL.98 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:R.44, H2O.29, H2O.29, H2O.41 CA.113: 3 residues within 4Å: Chain M: T.136, N.198, V.199 5 PLIP interactions: 2 interactions with chain M, 3 Ligand-Water interactions Metal complexes: M:T.136, M:V.199, H2O.35, H2O.36, H2O.36

6 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.43: 20 residues within 4Å: Chain B: Y.39, T.326, G.327, P.328, K.331, F.452, V.456 Chain D: I.274 Chain K: F.35 Chain L: N.4, L.6, A.10, L.13, F.14 Ligands: CLA.30, CLA.36, BCR.40, BCR.41, LHG.109, LMT.112 14 PLIP interactions: 1 interactions with chain D, 5 interactions with chain L, 2 interactions with chain K, 6 interactions with chain B Hydrophobic interactions: D:I.274, L:L.13, L:F.14, K:F.35, K:F.35, B:T.326, B:F.452, B:V.456 Hydrogen bonds: L:N.4, B:T.326, B:T.326 Water bridges: L:N.4, L:N.4, B:K.331 LMG.53: 21 residues within 4Å: Chain A: F.93, W.97, E.98, F.117, L.120, S.124, F.155 Chain C: L.195, L.196, K.197, S.198, F.200, E.203, W.205, F.266 Chain H: K.5, Y.9 Ligands: CLA.9, CLA.59, CLA.60, DGD.69 17 PLIP interactions: 6 interactions with chain C, 4 interactions with chain H, 7 interactions with chain A Hydrophobic interactions: C:F.200, C:W.205, C:F.266, A:F.93, A:F.93, A:F.117, A:L.120, A:F.155 Hydrogen bonds: C:E.203, H:K.5, H:K.5, H:Y.9, H:Y.9, A:W.97, A:E.98 Water bridges: C:S.198, C:S.198 LMG.72: 12 residues within 4Å: Chain C: F.52, H.56, Q.66 Chain J: D.14, V.18, V.21 Chain Q: Q.5, I.9 Ligands: CLA.58, CLA.62, DGD.70, UNL.104 5 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: Q:I.9, J:V.18, J:V.18, J:V.21 Salt bridges: C:H.56 LMG.73: 12 residues within 4Å: Chain C: W.79, D.89, F.91, P.92, V.95, V.99, H.100, S.103 Chain S: F.59 Ligands: CLA.57, CLA.67, BCR.78 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.79, C:P.92, C:V.95, C:V.99, C:V.99 Hydrogen bonds: C:D.89 LMG.102: 18 residues within 4Å: Chain D: Y.57, G.60, C.61, N.62, F.63 Chain F: T.29, I.36, M.39, Q.40 Chain I: F.27, G.30, A.31, L.35, G.36 Ligands: CLA.7, DGD.71, BCR.84, MG.103 11 PLIP interactions: 5 interactions with chain D, 3 interactions with chain F, 3 interactions with chain I Hydrophobic interactions: D:F.63, D:F.63, D:F.63, F:T.29 Hydrogen bonds: D:F.63, F:M.39, F:Q.40, I:G.30 Water bridges: D:N.62, I:F.27, I:G.36 LMG.124: 12 residues within 4Å: Chain C: A.105, F.109, Y.113 Chain S: M.19, Y.27, W.33, K.37, F.41, W.47 Ligands: CLA.65, CLA.67, BCR.107 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain S Hydrophobic interactions: C:A.105, C:F.109, C:F.109, C:F.109, S:M.19, S:F.41, S:W.47, S:W.47 Hydrogen bonds: C:Y.113, S:K.37 Salt bridges: S:K.37

5 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)

DGD.69: 29 residues within 4Å: Chain A: L.91, S.148, F.155, I.163 Chain C: P.199, F.200, G.201, G.202, E.203, G.204, W.205, V.207, S.208, V.209, N.210, M.263, F.266, C.270, F.274, N.275, N.276, T.277, D.342, F.343, R.344, F.417, L.420 Ligands: CLA.9, LMG.53 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.200, C:F.200, C:W.205, C:V.207, C:F.266, C:F.266, C:F.417, C:L.420, A:F.155, A:F.155, A:I.163 Hydrogen bonds: C:G.202, C:N.276, C:T.277, C:T.277, C:T.277, C:D.342, C:D.342, C:R.344, C:R.344 Water bridges: C:F.200 DGD.70: 19 residues within 4Å: Chain A: F.197, L.297 Chain C: E.65, Q.66, G.67, S.388, N.400, F.401, V.402, W.407, T.410, S.411, V.414 Chain I: Y.32 Ligands: CLA.58, CLA.62, DGD.71, LMG.72, UNL.104 16 PLIP interactions: 12 interactions with chain C, 2 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: C:W.407, C:V.414, A:F.197, A:L.297 Hydrogen bonds: C:E.65, C:S.388, C:N.400, C:N.400, C:V.402, C:V.402, C:W.407 Water bridges: C:E.65, C:Q.66, C:G.67, I:Y.32, I:Y.32 DGD.71: 32 residues within 4Å: Chain A: P.196, Q.199, L.200, A.203, W.278, F.285, F.300, N.301, F.302, S.305 Chain C: N.387, S.388, V.389, N.397, S.398, V.399, N.400 Chain D: N.62, L.64 Chain I: F.28, A.31, Y.32, G.36, S.37, S.38 Chain P: Q.34 Ligands: CLA.7, CLA.58, CLA.62, DGD.70, LHG.89, LMG.102 21 PLIP interactions: 8 interactions with chain A, 6 interactions with chain C, 4 interactions with chain I, 1 interactions with chain D, 2 interactions with chain P Hydrophobic interactions: A:P.196, A:L.200, A:A.203, A:W.278, A:F.285, A:F.300, A:F.300, I:F.28, D:L.64 Hydrogen bonds: A:S.305, C:N.387, C:N.397, C:S.398, C:V.399, I:G.36, P:Q.34, P:Q.34 Water bridges: C:N.397, C:N.400, I:Y.32, I:S.38 DGD.86: 9 residues within 4Å: Chain D: L.82, G.89, D.90, F.91, T.92 Chain E: D.45 Ligands: CLA.83, BCR.84, SQD.95 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain D Water bridges: E:R.51 Hydrophobic interactions: D:L.82, D:F.91, D:F.91, D:F.91 Hydrogen bonds: D:T.92 DGD.100: 22 residues within 4Å: Chain B: Y.192, F.249, G.253, Y.257, Y.272, Q.273, S.276, Y.278, F.462 Chain D: G.76, H.77, I.113, I.149, L.152, G.153 Chain G: L.45, Y.48, N.49, V.59, S.60, W.61 Ligands: CLA.25 21 PLIP interactions: 6 interactions with chain B, 5 interactions with chain D, 10 interactions with chain G Hydrophobic interactions: B:F.249, B:Y.257, B:F.462, D:I.113, D:I.149, D:L.152, D:L.152, G:Y.48, G:Y.48, G:Y.48 Hydrogen bonds: B:Y.192, D:H.77, G:N.49, G:V.59, G:S.60, G:W.61 Water bridges: B:Y.192, B:Y.192, G:S.50, G:S.60, G:S.60

5 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.87: 23 residues within 4Å: Chain A: S.232, N.234 Chain B: W.4, Y.5, R.6, L.460, F.463, W.467 Chain D: Y.131, I.134, W.256, F.259, L.262, F.263, V.266, W.270 Chain K: L.23 Chain L: F.14, P.18 Ligands: CLA.30, CLA.34, CLA.36, LHG.109 20 PLIP interactions: 8 interactions with chain D, 9 interactions with chain B, 1 interactions with chain L, 2 interactions with chain A Hydrophobic interactions: D:L.262, D:F.263, D:F.263, D:V.266, D:W.270, B:W.4, B:W.4, B:L.460, B:F.463, L:P.18 Hydrogen bonds: D:Y.131, A:S.232, A:N.234 Water bridges: D:R.129, D:Y.131, B:Y.5, B:R.6, B:R.6, B:R.6 Salt bridges: B:R.6 LHG.88: 26 residues within 4Å: Chain A: M.37 Chain D: I.246, F.247, I.249, A.250, F.251, S.252, N.253, W.256, F.260 Chain K: N.13, T.15, S.16, Y.18, L.19, L.22, L.29 Chain N: F.17, A.20, I.21 Ligands: CLA.6, PHO.8, CLA.80, PL9.85, LHG.109, GOL.115 19 PLIP interactions: 8 interactions with chain D, 5 interactions with chain N, 6 interactions with chain K Hydrophobic interactions: D:F.247, D:I.249, D:F.251, D:F.251, D:F.260, N:F.17, N:F.17, N:F.17, N:A.20, N:I.21, K:Y.18, K:L.22, K:L.22, K:L.29 Hydrogen bonds: D:S.252, D:S.252, D:N.253, K:N.13, K:S.16 LHG.89: 25 residues within 4Å: Chain A: R.140, W.142, A.146, L.200, F.273, V.281, W.284, F.285 Chain C: F.15, W.18, A.19, W.425, R.429 Chain D: E.209, N.210, A.219, S.220, T.221, F.222 Ligands: SQD.11, CLA.58, CLA.62, CLA.64, DGD.71, UNL.105 17 PLIP interactions: 9 interactions with chain A, 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: A:W.142, A:A.146, A:L.200, A:V.281, A:W.284, A:F.285, C:W.18, C:W.18 Water bridges: A:R.140, A:R.140 Salt bridges: A:R.140 Hydrogen bonds: D:N.210, D:A.219, D:S.220, D:T.221, C:R.429, C:R.429 LHG.93: 18 residues within 4Å: Chain A: L.258, I.259, F.260, Y.262, A.263 Chain D: F.17, L.27, F.28 Chain E: T.4, T.5, E.7, R.8, P.9, F.10, S.11 Chain F: R.18, A.21 Ligands: PL9.16 17 PLIP interactions: 9 interactions with chain E, 3 interactions with chain D, 3 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: E:F.10, D:F.17, D:L.27, D:F.28, A:F.260, A:F.260, A:A.263, F:A.21 Hydrogen bonds: E:T.4, E:T.4, E:T.5, E:G.6, E:E.7, E:E.7, E:F.10, E:S.11, F:R.18 LHG.109: 25 residues within 4Å: Chain A: S.232, N.234 Chain B: P.3, W.4, Y.5 Chain D: W.256, F.263 Chain K: E.11, L.12, N.13, S.16, L.19, G.20, L.22, V.26 Chain L: V.17, P.18, F.21 Ligands: CLA.34, CLA.37, LMG.43, CLA.80, PL9.85, LHG.87, LHG.88 14 PLIP interactions: 3 interactions with chain L, 1 interactions with chain D, 5 interactions with chain K, 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: L:V.17, L:P.18, L:F.21, D:F.263, K:L.22, K:V.26 Hydrogen bonds: K:E.11, K:N.13, K:S.16, A:S.232, A:S.232, A:N.234, B:W.4, B:Y.5

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.94: 15 residues within 4Å: Chain E: F.10, I.13, R.18, Y.19, H.23, T.26, I.27, L.30 Chain F: R.18, W.19, V.22, H.23, A.26, V.27, I.30 16 PLIP interactions: 8 interactions with chain F, 8 interactions with chain E, Hydrophobic interactions: F:W.19, F:V.22, F:A.26, F:V.27, E:F.10, E:I.13, E:T.26, E:I.27, E:I.27 Salt bridges: F:R.18, E:R.18 pi-Stacking: F:W.19, F:W.19, E:Y.19 Metal complexes: F:H.23, E:H.23

1 x MG: MAGNESIUM ION(Non-covalent)

MG.103: 5 residues within 4Å: Chain I: G.30, A.33, G.34, L.35 Ligands: LMG.102 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:G.30, I:A.33, I:L.35, H2O.29

1 x HEC: HEME C(Covalent)

HEC.118: 25 residues within 4Å: Chain P: A.36, C.37, S.39, C.40, H.41, T.46, T.48, L.52, D.53, L.54, T.58, L.59, A.62, L.72, Y.75, M.76, T.81, Y.82, I.88, H.92, P.93, M.104, I.115, I.119 Ligands: GOL.77 16 PLIP interactions: 16 interactions with chain P, Hydrophobic interactions: P:A.36, P:T.46, P:L.52, P:L.54, P:L.72, P:Y.75, P:Y.75, P:I.88, P:P.93, P:I.115, P:I.119 Hydrogen bonds: P:D.53, P:Y.82 pi-Stacking: P:Y.75 Metal complexes: P:H.41, P:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suga, M. et al., Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses. Nature (2015)

Release Date

2014-12-03

Peptides

Photosystem Q(B) protein: A
Photosystem II CP47 chlorophyll apoprotein: B
Photosystem II 44 kDa reaction center protein: C
Photosystem II D2 protein: D
Cytochrome b559 subunit alpha: E
Cytochrome b559 subunit beta: F
Photosystem II reaction center protein H: G
Photosystem II reaction center protein I: H
Photosystem II reaction center protein J: I
Photosystem II reaction center protein K: J
Photosystem II reaction center protein L: K
Photosystem II reaction center protein M: L
Photosystem II manganese-stabilizing polypeptide: M
Photosystem II reaction center protein T: N
Photosystem II 12 kDa extrinsic protein: O
Cytochrome c-550: P
Photosystem II reaction center protein Ycf12: Q
Photosystem II reaction center protein X: R
Photosystem II reaction center protein Z: S

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

C
c

D
d

E
e

F
f

G
h

H
i

I
j

J
k

K
l

L
m

M
o

N
t

O
u

P
v

Q
y

R
x

S
z

Membrane

We predict this structure to be a membrane protein.
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Photosystem Q(B) protein

Photosystem II CP47 chlorophyll apoprotein

Photosystem II 44 kDa reaction center protein

Photosystem II D2 protein

Cytochrome b559 subunit alpha

Cytochrome b559 subunit beta

Photosystem II reaction center protein H

Photosystem II reaction center protein I

Photosystem II reaction center protein J

Photosystem II reaction center protein K

Photosystem II reaction center protein L

Photosystem II reaction center protein M