SMTL ID : 5ws6.1 (1 other biounit)

Native XFEL structure of Photosystem II (preflash two-flash dataset

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

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

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: H.215, H.272 Chain D: H.204, H.258 Ligands: BCT.3 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

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

CL.2: 4 residues within 4Å: Chain A: N.181, H.332, E.333 Chain D: K.307 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: H.337, N.338, F.339 Chain C: G.335, E.336 Ligand excluded by PLIP

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

BCT.3: 10 residues within 4Å: Chain A: H.215, V.219, E.244, Y.246, H.272 Chain D: H.204, Y.234, K.254, H.258 Ligands: FE2.1 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.234, D:K.254

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.4: 28 residues within 4Å: Chain A: F.119, Y.147, P.150, S.153, V.157, F.182, M.183, I.184, F.186, Q.187, I.192, L.193, H.198, G.201, V.202, V.205, F.206, A.286, A.287, I.290 Chain D: L.172, L.195 Chain N: F.17 Ligands: CLA.5, CLA.6, PHO.7, CLA.75, LHG.79 18 PLIP interactions: 15 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:F.186, A:Q.187, A:I.192, A:I.192, A:L.193, A:L.193, A:V.205, A:F.206, A:F.206, A:I.290, N:F.17, D:L.172, D:L.195 Water bridges: A:I.290 Metal complexes: A:H.198 CLA.5: 20 residues within 4Å: Chain A: 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 Ligands: CLA.4, PHO.7, SQD.13, CLA.75, PL9.78, LHG.79, LHG.98 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.157, A:F.158, A:F.180, A:F.182, D:V.191 Metal complexes: H2O.4 CLA.6: 20 residues within 4Å: Chain A: Q.199, V.202, A.203, F.206, G.207, L.210, W.278 Chain D: F.147, V.165, I.168, F.169, F.171, L.172 Ligands: CLA.4, PHO.8, PL9.16, DGD.68, CLA.75, LHG.85, LMG.93 12 PLIP interactions: 4 interactions with chain A, 7 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.202, A:L.210, A:W.278, D:F.147, D:F.147, D:I.168, D:F.169, D:F.171, D:L.172, D:L.172 pi-Stacking: A:F.206 Metal complexes: H2O.5 CLA.9: 26 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.20 Ligands: BCR.10, UNL.17, LMG.18, CLA.55, CLA.56, DGD.66 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain H, Hydrophobic interactions: A:I.36, A:P.39, 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:F.117, A:L.121, H:Y.9, H:V.11, H:V.12, H:F.15, H:F.15, H:V.20 Hydrogen bonds: A:I.96 Salt bridges: A:H.118 Metal complexes: A:H.118 CLA.21: 11 residues within 4Å: Chain B: W.184, G.185, P.186, F.189 Chain G: F.40, I.43, I.47, L.54 Ligands: CLA.22, HTG.45, BCR.89 11 PLIP interactions: 5 interactions with chain G, 5 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: G:F.40, G:F.40, G:I.43, G:I.47, G:L.54, B:W.184, B:P.186, B:F.189, B:F.189, B:F.189 Metal complexes: H2O.7 CLA.22: 30 residues within 4Å: Chain B: E.183, 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, T.254 Chain D: L.148, I.149, L.152 Chain G: F.37, F.40, I.44, L.45, Y.48 Ligands: CLA.21, CLA.23, CLA.25, CLA.28, CLA.29, BCR.89, DGD.90 23 PLIP interactions: 3 interactions with chain D, 15 interactions with chain B, 5 interactions with chain G, Hydrophobic interactions: D:L.148, D:I.149, D:L.152, B:F.189, B:F.189, B:F.189, B:A.199, B:H.200, B:A.203, B:V.207, B:V.207, B:F.245, B:F.249, B:F.249, B:V.250, G:F.37, G:F.40, G:I.44, G:I.44 Water bridges: B:S.259 pi-Stacking: B:F.189, G:F.40 Metal complexes: B:H.200 CLA.23: 23 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.251, T.261 Chain G: L.38, L.41 Ligands: CLA.22, CLA.24, CLA.25, CLA.26, CLA.28, CLA.29, CLA.30, BCR.89 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain G, Hydrophobic interactions: B:L.68, B:A.145, B:L.148, B:F.152, B:F.152, B:F.246, B:A.247, G:L.38, G:L.41 Hydrogen bonds: B:R.67 Salt bridges: B:R.67 pi-Stacking: B:F.152 pi-Cation interactions: B:H.200 Metal complexes: B:H.201 CLA.24: 25 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.23, CLA.25, CLA.27, CLA.31, CLA.32, CLA.33, CLA.35, BCR.38, UNL.49 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.32, B:F.64, B:F.64, B:L.144, B:L.147, B:L.148, B:V.244, B:A.247, B:V.251, B:F.457, B:F.457, B:F.461, B:F.461 Salt bridges: B:R.67 Metal complexes: B:H.454 CLA.25: 27 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, C.149, A.204 Ligands: CLA.22, CLA.23, CLA.24, CLA.26, CLA.29, CLA.30, CLA.32, CLA.35, BCR.39, UNL.49 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:T.26, B:V.29, B:W.32, B:A.33, B:L.68, B:V.95, B:L.102, B:L.142 Water bridges: B:R.67 Salt bridges: B:R.67 Metal complexes: B:H.99 CLA.26: 23 residues within 4Å: Chain B: L.68, G.69, V.70, W.90, V.95, A.98, H.99, V.101, L.102, L.105, L.148, G.151, F.152, F.155, H.156, F.161, G.162, P.163 Ligands: CLA.23, CLA.25, CLA.36, BCR.39, UNL.49 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.68, B:W.90, B:V.101, B:L.102, B:L.105, B:L.148, B:F.155, B:F.161, B:F.161 Metal complexes: B:H.156 CLA.27: 25 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, H.454 Chain D: M.271 Chain K: F.31 Chain L: F.14 Ligands: CLA.24, CLA.33, BCR.37, BCR.38, LMG.41, LHG.84 12 PLIP interactions: 9 interactions with chain B, 1 interactions with chain K, 1 interactions with chain L, 1 Ligand-Water interactions, Hydrophobic interactions: B:W.32, B:Y.39, B:F.60, B:F.324, B:T.326, B:W.449, K:F.31, L:F.14 Hydrogen bonds: B:Y.39, B:G.327 pi-Stacking: B:F.60 Metal complexes: H2O.11 CLA.28: 28 residues within 4Å: Chain B: L.228, T.235, S.238, S.239, A.242, F.245, F.246, F.462, H.465, I.466, G.469, T.472, L.473 Chain D: L.79, F.110, I.113, M.116, L.117, F.120, I.140 Chain G: L.45 Ligands: CLA.22, CLA.23, CLA.29, CLA.30, CLA.76, UNL.82, DGD.90 21 PLIP interactions: 9 interactions with chain B, 1 interactions with chain G, 11 interactions with chain D, Hydrophobic interactions: B:A.242, B:F.245, B:F.246, B:F.462, B:F.462, B:I.466, B:L.473, G:L.45, D:L.79, D:F.110, D:F.110, D:F.110, D:I.113, D:I.113, D:M.116, D:L.117, D:F.120, D:F.120, D:I.140 Hydrogen bonds: B:S.238 Metal complexes: B:H.465 CLA.29: 27 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 D: F.110 Chain G: T.26, T.27, L.29, M.30, F.33, L.41, L.42 Ligands: CLA.22, CLA.23, CLA.25, CLA.28, CLA.30, UNL.82, BCR.89 18 PLIP interactions: 6 interactions with chain G, 11 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: G:L.29, G:M.30, G:F.33, G:L.41, G:L.42, B:F.138, B:F.138, B:L.142, B:V.207, B:A.211, B:F.214, B:F.214, B:L.224, B:L.228, D:F.110 Hydrogen bonds: G:T.26 Salt bridges: B:H.215 Metal complexes: B:H.215 CLA.30: 22 residues within 4Å: Chain B: H.22, L.134, M.137, F.138, H.141, L.142, A.145, L.228, M.230, I.233, T.235, V.236, S.239, S.240, A.243 Ligands: CLA.23, CLA.25, CLA.28, CLA.29, CLA.32, CLA.35, BCR.89 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.134, B:M.137, B:F.138, B:A.145, B:L.228, B:M.230, B:I.233, B:T.235 Hydrogen bonds: B:H.141 Metal complexes: H2O.6 CLA.31: 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, F.478 Ligands: CLA.24, CLA.32, CLA.33, CLA.34, LHG.84, LHG.98 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.4, B:V.7, B:H.8, B:T.9, B:L.237, B:L.237, B:I.241, B:F.457, B:F.461, 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.32: 20 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, V.244 Ligands: CLA.24, CLA.25, CLA.30, CLA.31, CLA.33, CLA.34, CLA.35 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:H.8, B:L.11, B:L.11, B:I.12, B:L.18, B:H.22, B:H.25, B:T.26, B:I.233, B:I.233, B:V.236, B:L.237, 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.33: 15 residues within 4Å: Chain B: H.8, H.25, V.29, W.32, F.461 Chain L: F.14 Ligands: CLA.24, CLA.27, CLA.31, CLA.32, CLA.34, BCR.37, BCR.38, LMG.41, LHG.84 11 PLIP interactions: 1 interactions with chain L, 10 interactions with chain B, Hydrophobic interactions: L:F.14, 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, B:H.8 Metal complexes: B:H.25 CLA.34: 20 residues within 4Å: Chain B: L.2, 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: CLA.31, CLA.32, CLA.33, BCR.37, SQD.40, LMG.41, LHG.98 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain L, Hydrophobic interactions: B:V.7, B:V.7, B:L.11, B:A.21, B:M.24, B:L.28, B:W.114, L:F.21, L:L.25 Metal complexes: B:H.8 CLA.35: 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.24, CLA.25, CLA.30, CLA.32, CLA.36, BCR.39 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain G, Hydrophobic interactions: B:I.19, B:L.132, B:I.140, B:L.144, G:L.6, G:L.10, G:L.10, G:L.13, G:L.13 Hydrogen bonds: B:H.22 Metal complexes: B:H.141 CLA.36: 15 residues within 4Å: Chain B: I.19, L.23, A.109, W.112, H.113, L.119, L.121 Chain G: T.4, L.6, G.7, L.10 Ligands: CLA.26, CLA.35, BCR.39, UNL.49 10 PLIP interactions: 3 interactions with chain G, 7 interactions with chain B, Hydrophobic interactions: G:L.6, G:L.10, B:I.19, B:L.23, B:W.112, B:W.112, B:L.119 Hydrogen bonds: G:T.4 pi-Stacking: B:W.112 Metal complexes: B:H.113 CLA.51: 20 residues within 4Å: Chain C: T.76, L.77, L.150, G.153, A.154, L.157, I.206, V.215, H.219, I.222, A.260, M.264, F.271, V.278, Y.279 Ligands: CLA.52, CLA.53, CLA.56, CLA.57, BCR.65 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:I.206, C:I.222, C:I.222, C:A.260, C:M.264, C:F.271, C:V.278 Metal complexes: C:H.219 CLA.52: 26 residues within 4Å: Chain C: W.45, I.69, L.70, H.73, L.77, W.79, G.153, 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.51, CLA.53, CLA.54, CLA.60, CLA.62, LMG.69, HTG.71 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:W.45, C:I.69, C:L.70, C:L.77, C:W.79, C:L.156, C:F.164, C:L.261, C:M.264, C:A.268, C:L.408, C:F.419 Hydrogen bonds: C:Y.279 Salt bridges: C:H.73, C:H.412 Metal complexes: C:H.412 CLA.53: 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.51, CLA.52, CLA.57, CLA.59, CLA.60, CLA.62, CLA.63, LMG.70 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.54: 20 residues within 4Å: Chain C: W.45, M.49, F.52, Q.66, G.67, I.69, W.407, L.408, S.411, H.412, F.418 Chain J: P.17, V.21 Ligands: CLA.52, CLA.58, CLA.60, DGD.67, DGD.68, LMG.69, LHG.80 13 PLIP interactions: 11 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:L.408, C:F.418, C:F.418, C:F.418, J:V.21 Hydrogen bonds: C:S.388 pi-Stacking: C:W.407 Metal complexes: H2O.17 CLA.55: 23 residues within 4Å: Chain A: F.33, S.124, M.127, G.128, W.131 Chain C: F.246, S.255, Y.256, G.259, A.260, L.420, H.423, L.424, A.427, R.431 Chain H: V.16, F.19, F.23 Ligands: CLA.9, LMG.18, CLA.57, BCR.65, DGD.66 18 PLIP interactions: 10 interactions with chain C, 5 interactions with chain A, 3 interactions with chain H, Hydrophobic interactions: C:F.246, C:Y.256, C:Y.256, C:L.420, C:L.424, A:F.33, A:W.131, A:W.131, A:W.131, H:V.16, H:F.19, H:F.23 Hydrogen bonds: C:R.431 Water bridges: C:I.247, C:I.247 Salt bridges: C:R.431 Metal complexes: C:H.423 pi-Stacking: A:W.131 CLA.56: 21 residues within 4Å: Chain C: L.143, L.147, L.195, W.205, 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, CLA.51, CLA.57, BCR.65, DGD.66, LMT.91 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.143, C:L.147, C:L.147, C:L.195, C:W.205, C:W.232, C:W.241 Hydrogen bonds: C:F.239 Salt bridges: C:H.233 Metal complexes: C:H.233 CLA.57: 20 residues within 4Å: Chain C: M.139, T.140, L.143, H.146, L.147, L.150, F.246, W.248, Y.253, Y.256, S.257, A.260, L.261, M.264 Ligands: CLA.51, CLA.53, CLA.55, CLA.56, CLA.59, BCR.65 18 PLIP interactions: 17 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:M.139, C:T.140, C:L.143, C:L.143, C:L.150, C:F.246, C:F.246, C:F.246, C:W.248, C:W.248, C:Y.253, C:Y.253, C:Y.256, C:Y.256, C:A.260, C:L.261 Hydrogen bonds: C:H.146 Metal complexes: H2O.13 CLA.58: 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 Chain J: V.21 Ligands: SQD.11, CLA.54, CLA.59, CLA.60, CLA.61, DGD.67, LMG.69, LHG.80 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain J, Hydrophobic interactions: C:L.258, C:F.419, C:F.419, C:W.425, J:V.21 Hydrogen bonds: C:N.21 Salt bridges: C:H.426, C:R.429 pi-Stacking: C:W.425 Metal complexes: C:H.426 CLA.59: 25 residues within 4Å: Chain C: N.21, L.24, I.25, L.31, A.34, H.35, H.38, Y.131, W.133, M.139, I.142, H.146, G.250, E.251, Y.253, L.254, S.257, L.258, L.261 Ligands: CLA.53, CLA.57, CLA.58, CLA.60, CLA.61, CLA.62 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:N.21, C:L.24, C:I.25, C:L.31, C:A.34, C:H.38, C:W.133, C:W.133, C:W.133, C:I.142, C:Y.253 Hydrogen bonds: C:S.257 Metal complexes: C:H.35 CLA.60: 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.52, CLA.53, CLA.54, CLA.58, CLA.59, CLA.61, LHG.80 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.61: 34 residues within 4Å: Chain C: T.6, N.7, R.8, W.17, G.20, N.21, R.23, L.24, L.27, K.30, A.34, H.38, G.108, F.109 Chain J: F.23, L.24, A.27, W.30, Q.31 Chain R: I.19, I.20, L.23, N.29, L.30 Chain S: M.19, V.20, V.23, P.24, A.28 Ligands: CLA.58, CLA.59, CLA.60, BCR.97, LMG.110 22 PLIP interactions: 8 interactions with chain J, 7 interactions with chain C, 3 interactions with chain R, 4 interactions with chain S, Hydrophobic interactions: J:F.23, J:F.23, J:L.24, J:A.27, J:W.30, J:Q.31, C:W.17, C:L.24, C:L.24, C:F.109, R:I.19, R:I.20, R:L.30, 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 Water bridges: C:R.8 Salt bridges: C:R.8 CLA.62: 19 residues within 4Å: Chain C: 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, L.156 Ligands: CLA.52, CLA.53, CLA.59, CLA.63, BCR.64 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:H.35, C:F.128, C:Y.131, C:I.142, C:F.145, C:F.145, C:F.145, C:I.148, C:V.149, C:I.152, C:L.156 Metal complexes: C:H.146 CLA.63: 16 residues within 4Å: Chain C: L.32, V.36, V.106, L.107, G.110, Y.113, H.114, P.119, L.122, Y.125, F.129 Ligands: CLA.53, CLA.62, BCR.64, LMG.70, LMG.110 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.32, C:L.32, C:V.36, C:V.106, C:L.107, C:Y.113, C:L.122, C:Y.125, C:F.129, C:F.129, C:F.129, C:F.129 Hydrogen bonds: C:Y.113 Salt bridges: C:H.114 pi-Stacking: C:F.129 Metal complexes: C:H.114 CLA.75: 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.4, CLA.5, CLA.6, PHO.8, PL9.16 18 PLIP interactions: 18 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.191, D:V.194, D:V.194, D:L.195, D:L.269 pi-Stacking: D:W.181 Metal complexes: D:H.187 CLA.76: 26 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: L.38, L.42 Chain Q: F.10, G.12, L.13, G.16, A.17, V.19 Ligands: PL9.16, CLA.28, UNL.108 17 PLIP interactions: 12 interactions with chain D, 3 interactions with chain Q, 2 interactions with chain G, Hydrophobic interactions: D:L.26, D:P.29, D:L.33, D:L.81, D:L.82, D:W.83, D:W.83, D:L.106, Q:F.10, Q:L.13, Q:V.19, G:L.38, G:L.42 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.7: 25 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, V.205, P.279, V.283 Chain D: L.195, A.198, L.199, I.203, W.243, F.247 Ligands: CLA.4, CLA.5 19 PLIP interactions: 16 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:F.119, A:Y.126, A:A.146, A:Y.147, A:Y.147, A:P.150, A:F.158, A:V.205, A:P.279, D:L.195, D:A.198, D:L.199 Hydrogen bonds: A:Y.126, A:Q.130 PHO.8: 32 residues within 4Å: Chain A: F.206, A.209, L.210, A.213, M.214, F.255, L.258, I.259 Chain D: L.27, A.31, L.35, W.38, I.104, G.108, G.111, L.112, F.115, Q.119, N.132, A.135, F.136, P.139, F.143, F.163, G.164, V.165, P.265, V.266, L.269 Ligands: CLA.6, PL9.16, CLA.75 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:A.31, D:L.35, 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:P.139, D:F.143, D:V.165, D:P.265, D:L.269, A:F.206, A:L.210, A:A.213 Hydrogen bonds: D:Q.119, D:N.132 pi-Stacking: D:F.136

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

BCR.10: 17 residues within 4Å: Chain A: F.17, V.35, P.39, L.42, A.43, I.46, C.47, I.50, A.51, A.55, I.96, W.105, L.106 Chain H: F.15 Ligands: CLA.9, UNL.17, UNL.92 9 PLIP interactions: 1 interactions with chain H, 8 interactions with chain A Hydrophobic interactions: H:F.15, A:F.17, A:P.39, A:I.46, A:I.50, A:A.51, A:I.96, A:W.105, A:L.106 BCR.37: 12 residues within 4Å: Chain B: M.24, L.28, C.111, W.114 Chain L: L.13 Ligands: CLA.27, CLA.33, CLA.34, BCR.38, SQD.40, LMG.41, LHG.98 6 PLIP interactions: 1 interactions with chain L, 5 interactions with chain B Hydrophobic interactions: L:L.13, B:L.28, B:L.28, B:W.114, B:W.114, B:W.114 BCR.38: 14 residues within 4Å: Chain B: L.28, G.31, W.32, S.35, I.100, V.101, S.103, G.104 Ligands: CLA.24, CLA.27, CLA.33, BCR.37, SQD.40, LMG.41 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.28, B:W.32 BCR.39: 12 residues within 4Å: Chain B: L.102, L.105, L.108, A.109, C.111, W.112, V.115 Ligands: CLA.25, CLA.26, CLA.35, CLA.36, UNL.49 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.102, B:W.112, B:V.115 BCR.64: 15 residues within 4Å: Chain C: F.94, V.98, I.102, S.103, V.106, L.107, F.129 Chain J: Y.6 Chain S: V.51, G.55, N.58, F.59 Ligands: CLA.62, CLA.63, LMG.70 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain S Hydrophobic interactions: C:F.94, C:V.98, C:I.102, C:V.106, C:V.106, C:V.106, C:L.107, C:F.129, S:V.51, S:N.58, S:F.59 BCR.65: 19 residues within 4Å: Chain C: I.191, F.192, Y.194, L.195, I.206, V.209, D.214, V.215, G.218, H.219, I.222, F.246 Chain H: V.20, F.23, L.24 Ligands: CLA.51, CLA.55, CLA.56, CLA.57 12 PLIP interactions: 2 interactions with chain H, 10 interactions with chain C Hydrophobic interactions: H:F.23, H:L.24, 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 BCR.77: 16 residues within 4Å: Chain D: Y.32, L.33, G.36, G.37, L.39, T.40, F.91 Chain F: P.28, T.29, F.32, L.33, I.36 Chain I: V.20, V.24 Ligands: DGD.67, LMG.93 13 PLIP interactions: 2 interactions with chain I, 7 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: I:V.20, I:V.24, F:P.28, F:T.29, F:F.32, F:F.32, F:F.32, F:L.33, F:I.36, D:Y.32, D:L.33, D:L.39, D:F.91 BCR.89: 17 residues within 4Å: Chain G: M.30, M.34, L.36, F.37, V.39, F.40, I.43, L.54 Chain Q: T.1, I.2, L.6, F.10 Ligands: CLA.21, CLA.22, CLA.23, CLA.29, CLA.30 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain Q Hydrophobic interactions: G:L.36, G:F.37, G:F.37, G:F.37, G:F.37, G:V.39, G:F.40, G:I.43, G:L.54, Q:L.6, Q:F.10 BCR.97: 18 residues within 4Å: Chain C: A.37, G.40, L.41, L.101, S.104, A.105, G.108, A.115 Chain J: Y.6, F.9, L.16, F.23, W.30 Chain S: L.9, L.12, S.16 Ligands: CLA.61, BCR.109 13 PLIP interactions: 5 interactions with chain C, 6 interactions with chain J, 2 interactions with chain S Hydrophobic interactions: C:A.37, C:L.41, C:L.101, C:A.105, C:A.115, J:Y.6, J:F.9, J:L.16, J:F.23, J:F.23, J:W.30, S:L.9, S:L.12 BCR.103: 11 residues within 4Å: Chain A: L.28 Chain N: I.4, F.8, A.11, I.14, A.15, F.17, F.18, I.21, F.22 Ligands: SQD.13 11 PLIP interactions: 10 interactions with chain N, 1 interactions with chain A Hydrophobic interactions: N:I.4, N:F.8, N:A.11, N:I.14, N:F.17, N:F.18, N:F.18, N:I.21, N:F.22, N:F.22, A:L.28 BCR.109: 22 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, V.29 Chain R: I.12, G.13, G.16, P.17 Chain S: V.13, S.16, F.17 Ligands: SQD.11, UNL.96, BCR.97 13 PLIP interactions: 8 interactions with chain J, 3 interactions with chain R, 1 interactions with chain S, 1 interactions with chain C Hydrophobic interactions: J:L.12, J:L.16, J:I.19, J:I.19, J:L.22, J:F.23, J:A.25, J:V.29, R:I.12, R:I.12, R:P.17, S:F.17, C:F.44

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

SQD.11: 24 residues within 4Å: Chain A: L.200, A.203, G.204, N.267, S.270, F.273, F.274, A.277, W.278, V.281 Chain C: Q.10, A.16, W.18 Chain D: S.220, F.222, R.223 Chain I: I.21 Chain J: A.25, F.28 Ligands: CLA.58, LMG.69, LHG.80, UNL.96, BCR.109 18 PLIP interactions: 11 interactions with chain A, 2 interactions with chain C, 1 interactions with chain I, 2 interactions with chain J, 2 interactions with chain D Hydrophobic interactions: A:A.203, A:F.273, A:F.274, A:A.277, A:W.278, A:W.278, A:V.281, C:W.18, I:I.21, J:A.25, J:F.28 Hydrogen bonds: A:N.267, A:S.270, C:Q.10, D:S.220, D:S.220 Water bridges: A:N.266, A:N.267 SQD.13: 13 residues within 4Å: Chain A: W.20, N.26, R.27, L.28, V.30, L.42, T.45 Chain N: F.22 Ligands: CLA.5, UNL.17, LHG.79, UNL.92, BCR.103 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.26, A:L.28, A:V.30, A:L.42, A:T.45 Hydrogen bonds: A:N.26, A:R.27, A:L.28 SQD.40: 8 residues within 4Å: Chain B: R.17, L.28, S.103, W.114 Chain K: R.7 Ligands: CLA.34, BCR.37, BCR.38 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain K Hydrophobic interactions: B:L.28 Salt bridges: B:R.17, K:R.7 SQD.88: 13 residues within 4Å: Chain D: R.14, R.16 Chain E: E.7 Chain F: F.15, T.16, V.17, V.20 Chain Q: T.23, I.30, D.34 Chain T: Q.29, L.33 Ligands: PL9.16 11 PLIP interactions: 2 interactions with chain Q, 3 interactions with chain D, 4 interactions with chain F, 1 interactions with chain T, 1 interactions with chain E Hydrophobic interactions: Q:I.30, F:V.17, F:V.20 Hydrogen bonds: Q:D.34, D:R.14, F:V.17, T:Q.29, E:E.7 Salt bridges: D:R.14, D:R.16 Water bridges: F:R.18

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 1 residues within 4Å: Chain A: D.103 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.103, A:D.103, A:D.103 GOL.46: 8 residues within 4Å: Chain B: W.274, D.275, S.277, R.356, R.357, M.358, P.359 Chain D: E.327 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:E.327, B:W.274, B:S.277, B:R.356, B:R.356 Water bridges: B:S.277 GOL.47: 7 residues within 4Å: Chain B: P.49, P.53, M.54, I.79, W.166, E.265, K.307 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.54, B:K.307, B:K.307 Water bridges: B:E.265, B:K.307 GOL.74: 9 residues within 4Å: Chain A: L.341 Chain C: M.378, T.379, H.380, A.381, G.391, V.392, E.395 Chain P: K.47 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain P Hydrogen bonds: C:M.378, C:A.381, C:V.392, P:K.47 Water bridges: C:T.379, P:S.39, P:K.47, P:K.47 GOL.105: 6 residues within 4Å: Chain C: E.395 Chain O: K.104 Chain P: I.45, G.133, K.134, Y.137 7 PLIP interactions: 3 interactions with chain O, 1 interactions with chain C, 3 interactions with chain P Water bridges: O:K.104, O:K.104, O:K.104, P:K.134, P:K.134 Hydrogen bonds: C:E.395, P:K.134

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

OEX.14: 10 residues within 4Å: Chain A: D.170, E.189, H.332, E.333, H.337, D.342, A.344 Chain C: E.336, R.339 Ligands: OEY.15 17 PLIP interactions: 9 interactions with chain A, 4 interactions with chain C, 4 Ligand-Water interactions 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, C:E.336, C:E.336, H2O.1, H2O.2, H2O.3, H2O.5 Hydrogen bonds: C:R.339, C:R.339

1 x OEY: CA-MN4-O6 CLUSTER(Covalent)

OEY.15: 11 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 Ligands: OEX.14 18 PLIP interactions: 10 interactions with chain A, 4 interactions with chain C, 4 Ligand-Water interactions Metal complexes: A:D.170, A:D.170, A:E.189, A:E.189, A:H.332, A:E.333, A:E.333, A:D.342, A:D.342, A:A.344, C:E.336, C:E.336, H2O.1, H2O.2, H2O.3, H2O.5 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: 31 residues within 4Å: Chain A: F.211, M.214, H.215, L.218, V.219, Y.246, I.248, A.251, H.252, F.255, A.263, S.264, F.265, L.271, F.274, L.275 Chain D: F.28, P.29, A.31, L.35 Chain F: A.21, T.24, L.25 Chain Q: T.23, L.27 Ligands: CLA.6, PHO.8, CLA.75, CLA.76, LHG.85, SQD.88 22 PLIP interactions: 16 interactions with chain A, 3 interactions with chain D, 2 interactions with chain Q, 1 interactions with chain F Hydrophobic interactions: A:F.211, A:M.214, A:L.218, A:V.219, A:Y.246, A:I.248, A:A.251, A:F.255, A:F.255, A:F.255, A:L.271, A:L.271, A:F.274, A:L.275, D:F.28, D:A.31, D:L.35, Q:T.23, Q:L.27, F:L.25 Hydrogen bonds: A:H.215, A:F.265 PL9.78: 33 residues within 4Å: Chain A: V.49, F.52, I.53, I.77, I.176 Chain D: M.188, M.189, A.192, G.193, L.199, L.200, H.204, T.207, Y.234, 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: CLA.5, LHG.79, LHG.98 26 PLIP interactions: 15 interactions with chain D, 5 interactions with chain A, 4 interactions with chain N, 2 interactions with chain K Hydrophobic interactions: D:M.189, D:L.199, D:L.200, D:T.207, D:Y.234, D:W.243, D:F.251, D:F.251, D:F.251, D:L.257, D:F.260, D:F.263, D:V.264, A:V.49, A:F.52, A:I.53, A:I.77, A:I.176, N:F.10, N:F.10, N:F.10, N:F.10, K:L.23, K:L.29 Hydrogen bonds: D:H.204, D:F.251

9 x UNL: UNKNOWN LIGAND

UNL.17: 8 residues within 4Å: Chain A: L.13, R.16, F.17, W.20 Ligands: CLA.9, BCR.10, SQD.13, UNL.92 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.13, A:F.17, A:W.20 Salt bridges: A:R.16 UNL.49: 6 residues within 4Å: Chain B: W.90 Ligands: CLA.24, CLA.25, CLA.26, CLA.36, BCR.39 No protein-ligand interaction detected (PLIP) UNL.81: 8 residues within 4Å: Chain D: W.22, S.23, F.120, E.121 Chain G: L.38 Chain Q: L.20 Ligands: UNL.82, UNL.108 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain G, 1 interactions with chain Q Hydrophobic interactions: D:W.22, D:E.121, G:L.38, Q:L.20 UNL.82: 10 residues within 4Å: Chain B: A.227 Chain D: F.5, K.13, W.22, R.124 Chain Q: F.24 Ligands: CLA.28, CLA.29, LMT.42, UNL.81 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain Q Hydrophobic interactions: D:F.5, D:W.22, D:W.22, Q:F.24, Q:F.24 Hydrogen bonds: D:K.13 Salt bridges: D:K.13 UNL.92: 7 residues within 4Å: Chain H: M.1, T.3, L.4, T.7 Ligands: BCR.10, SQD.13, UNL.17 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:T.3, H:L.4, H:T.7 Hydrogen bonds: H:T.3 UNL.94: 6 residues within 4Å: Chain I: G.25, F.28, Y.29, Y.32 Ligands: DGD.67, LMG.69 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:F.28, I:Y.32 UNL.96: 5 residues within 4Å: Chain C: W.17 Chain J: F.36 Ligands: SQD.11, LHG.80, BCR.109 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:F.36 UNL.100: 2 residues within 4Å: Chain L: I.23 Ligands: LMT.99 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:I.23 UNL.108: 8 residues within 4Å: Chain D: L.82, W.83, G.89 Chain Q: S.15, G.16, L.20 Ligands: CLA.76, UNL.81 3 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain D Hydrophobic interactions: Q:L.20, D:L.82, D:W.83

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

LMG.18: 21 residues within 4Å: Chain A: F.93, W.97, E.98, F.117, L.121, S.124, F.155 Chain C: L.196, K.197, S.198, P.199, F.200, E.203, W.205, M.263, F.266 Chain H: K.5, Y.9 Ligands: CLA.9, CLA.55, DGD.66 16 PLIP interactions: 7 interactions with chain C, 1 interactions with chain H, 8 interactions with chain A Hydrophobic interactions: C:F.200, C:W.205, C:W.205, C:F.266, C:F.266, A:F.93, A:F.117, A:L.121, A:L.121, A:F.155, A:F.155 Hydrogen bonds: C:S.198, C:E.203, H:Y.9, A:W.97, A:E.98 LMG.41: 19 residues within 4Å: Chain B: Y.39, T.326, G.327, P.328, K.331 Chain D: I.274 Chain K: F.35 Chain L: N.4, L.6, A.10, L.13, F.14, V.17 Ligands: CLA.27, CLA.33, CLA.34, BCR.37, BCR.38, LHG.98 12 PLIP interactions: 2 interactions with chain K, 4 interactions with chain L, 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: K:F.35, K:F.35, L:L.13, L:F.14, L:V.17, D:I.274 Hydrogen bonds: L:N.4, B:Y.39, B:T.326, B:T.326 Water bridges: B:K.331, B:K.331 LMG.69: 15 residues within 4Å: Chain C: F.52, H.56, Q.66 Chain I: I.21 Chain J: D.14, V.18, V.21 Chain R: Q.5, I.9 Ligands: SQD.11, CLA.52, CLA.54, CLA.58, DGD.67, UNL.94 9 PLIP interactions: 1 interactions with chain I, 3 interactions with chain J, 3 interactions with chain C, 2 interactions with chain R Hydrophobic interactions: I:I.21, J:D.14, J:V.18, J:V.21, R:I.9 Hydrogen bonds: C:H.56, R:Q.5 Salt bridges: C:H.56, C:H.56 LMG.70: 14 residues within 4Å: Chain C: V.43, W.79, D.89, F.91, V.95, V.99, H.100, S.103 Chain S: F.59, V.62 Ligands: CLA.53, CLA.63, BCR.64, HTG.71 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.43, C:W.79, C:W.79, C:V.95, C:V.99 LMG.93: 17 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 Ligands: CLA.6, DGD.68, BCR.77, MG.95 13 PLIP interactions: 3 interactions with chain F, 6 interactions with chain D, 4 interactions with chain I Hydrophobic interactions: F:T.29, D:F.63, D:F.63, D:F.63, D:F.63, I:F.27 Hydrogen bonds: F:M.39, F:Q.40, D:F.63, I:G.30 Water bridges: D:N.62, I:F.27, I:G.36 LMG.110: 11 residues within 4Å: Chain C: F.109, Y.113, R.117 Chain S: Y.27, W.33, K.37, I.40, F.41, W.47 Ligands: CLA.61, CLA.63 10 PLIP interactions: 5 interactions with chain S, 5 interactions with chain C Hydrophobic interactions: S:I.40, S:F.41, S:W.47, S:W.47, C:F.109, C:F.109 Salt bridges: S:K.37 Hydrogen bonds: C:Y.113, C:R.117, C:R.117

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

LMT.20: 4 residues within 4Å: Chain A: L.72, Y.73 Chain D: R.294 Chain M: G.110 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D, 1 interactions with chain M Hydrophobic interactions: A:L.72 Hydrogen bonds: A:L.72, A:Y.73, D:R.294, D:R.294, M:G.110 LMT.42: 16 residues within 4Å: Chain B: R.223, L.224, K.226, K.497, D.500 Chain D: R.2, F.5, D.6, D.9, D.10 Chain G: W.24, M.30, A.31, M.34 Chain Q: R.38 Ligands: UNL.82 11 PLIP interactions: 5 interactions with chain B, 3 interactions with chain G, 1 interactions with chain Q, 2 interactions with chain D Hydrophobic interactions: B:L.224, G:W.24, G:W.24, G:A.31 Hydrogen bonds: B:K.497, B:D.500, Q:R.38, D:R.2, D:D.9 Salt bridges: B:R.223, B:K.497 LMT.50: 2 residues within 4Å: Chain B: S.35, A.42 No protein-ligand interaction detected (PLIP) LMT.86: 5 residues within 4Å: Chain E: W.35, S.39 Chain F: F.41, I.42, Q.43 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.41, E:W.35, E:W.35 Hydrogen bonds: F:Q.43, F:Q.43 LMT.91: 9 residues within 4Å: Chain A: W.14, E.15 Chain C: W.241, R.244 Chain H: L.24, S.25, G.26, R.30 Ligands: CLA.56 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: C:W.241 Hydrogen bonds: C:R.244, C:R.244, H:R.30 Water bridges: H:R.30 LMT.99: 6 residues within 4Å: Chain L: V.27, E.30, S.31, Q.32, Q.33 Ligands: UNL.100 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:E.30 LMT.101: 6 residues within 4Å: Chain L: M.1, E.2, Q.5, A.12 Chain N: I.4, F.8 6 PLIP interactions: 2 interactions with chain L, 4 interactions with chain N Hydrophobic interactions: L:A.12, N:I.4, N:I.4, N:F.8, N:F.8 Hydrogen bonds: L:Q.5

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

HTG.43: 6 residues within 4Å: Chain B: S.73, W.74, S.75, W.77, E.93, L.97 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.74, B:L.97 Hydrogen bonds: B:S.73, B:S.75, B:E.93 HTG.44: 12 residues within 4Å: Chain B: K.340, S.418, Y.419, K.422, F.429, E.430, F.431, T.433 Chain M: Q.174, A.175, K.176, E.177 10 PLIP interactions: 4 interactions with chain M, 6 interactions with chain B Hydrogen bonds: M:Q.174, M:K.176, B:K.340, B:K.340, B:K.422, B:E.430, B:F.431, B:F.431 Water bridges: M:E.177, M:E.177 HTG.45: 3 residues within 4Å: Chain B: W.184, I.206 Ligands: CLA.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.184, B:W.184, B:I.206 HTG.48: 5 residues within 4Å: Chain B: W.74, D.86, G.88, F.89, L.97 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.74, B:L.97 Hydrogen bonds: B:D.86, B:G.88, B:G.88 HTG.71: 5 residues within 4Å: Chain C: W.79, F.164, G.165 Ligands: CLA.52, LMG.70 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.79 HTG.72: 4 residues within 4Å: Chain C: F.163, N.183, P.184, L.186 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.183 HTG.83: 5 residues within 4Å: Chain D: G.3, W.4, F.5 Chain G: W.24, P.28 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: G:W.24 Hydrogen bonds: D:F.5 HTG.107: 6 residues within 4Å: Chain P: A.89, E.90, R.96, S.97, D.99, I.100 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:E.90, P:R.96, P:D.99

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

DGD.66: 32 residues within 4Å: Chain A: L.91, S.148, L.151, A.152, F.155, I.160, 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, F.266, C.270, F.274, N.275, N.276, T.277, D.342, F.343, R.344, L.420 Ligands: CLA.9, LMG.18, CLA.55, CLA.56 20 PLIP interactions: 4 interactions with chain A, 16 interactions with chain C Hydrophobic interactions: A:L.151, A:F.155, A:I.160, A:I.163, C:P.199, C:F.200, C:F.200, C:W.205, C:V.207, C:F.266 Hydrogen bonds: C:G.202, C:N.276, C:T.277, C:T.277, C:D.342, C:D.342, C:R.344, C:R.344 Water bridges: C:P.199, C:F.200 DGD.67: 20 residues within 4Å: Chain A: F.197, L.297 Chain C: E.65, Q.66, G.67, L.386, S.388, N.400, F.401, V.402, W.407, T.410 Chain I: F.28, Y.32 Ligands: CLA.54, CLA.58, DGD.68, LMG.69, BCR.77, UNL.94 17 PLIP interactions: 3 interactions with chain A, 11 interactions with chain C, 3 interactions with chain I Hydrophobic interactions: A:F.197, A:F.197, A:L.297, C:L.386, C:L.386, I:F.28, I:F.28 Hydrogen bonds: C:S.388, C:N.400, C:N.400, C:V.402, C:V.402, I:Y.32 Water bridges: C:E.65, C:Q.66, C:G.67, C:G.67 DGD.68: 29 residues within 4Å: Chain A: Q.199, L.200, A.203, W.278, F.300, N.301, F.302, S.305 Chain C: L.386, N.387, S.388, V.389, N.397, S.398, V.399, N.400 Chain D: N.62 Chain I: F.28, A.31, Y.32, G.36, S.37, S.38 Chain P: Q.34 Ligands: CLA.6, CLA.54, DGD.67, LHG.80, LMG.93 14 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C, 1 interactions with chain P, 3 interactions with chain I Hydrophobic interactions: A:Q.199, A:L.200, A:A.203, A:W.278, A:F.300 Hydrogen bonds: A:S.305, C:N.387, C:N.397, C:S.398, P:Q.34, I:G.36, I:S.38 Water bridges: C:N.400, I:G.36 DGD.90: 28 residues within 4Å: Chain B: Y.192, F.249, G.253, Y.257, Y.272, Q.273, S.276, Y.278, T.451, F.462 Chain D: G.76, H.77, F.110, I.113, I.149, L.152, G.153, S.155, A.280, L.281 Chain G: L.45, Y.48, N.49, V.59, S.60, W.61 Ligands: CLA.22, CLA.28 20 PLIP interactions: 7 interactions with chain D, 7 interactions with chain G, 6 interactions with chain B Hydrophobic interactions: D:F.110, D:I.113, D:I.149, D:A.280, D:L.281, G:Y.48, G:Y.48, G:Y.48, B:F.249, B:Y.257, B:T.451, B:F.462 Hydrogen bonds: D:H.77, D:S.155, G:N.49, G:V.59, G:S.60, G:W.61, B:Y.192, B:Y.192

3 x CA: CALCIUM ION(Non-covalent)

CA.73: 6 residues within 4Å: Chain C: N.137, T.140, T.141, H.233, I.234, T.236 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.137, C:T.140, C:T.141, C:H.233, C:T.236 CA.102: 5 residues within 4Å: Chain M: T.136, S.137, T.138, N.198, V.199 3 PLIP interactions: 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:T.136, M:V.199, H2O.25 CA.104: 3 residues within 4Å: Chain A: A.309 Chain F: R.44 Chain P: E.23 2 PLIP interactions: 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.23, H2O.31

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

LHG.79: 23 residues within 4Å: 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.29 Chain N: F.17, A.20, I.21 Ligands: CLA.4, CLA.5, SQD.13, PL9.78, LHG.98 16 PLIP interactions: 8 interactions with chain D, 5 interactions with chain K, 3 interactions with chain N Hydrophobic interactions: D:F.247, D:I.249, D:F.251, D:F.260, D:F.260, K:Y.18, K:L.29, N:F.17, N:F.17, N:I.21 Hydrogen bonds: D:S.252, D:S.252, D:N.253, K:N.13, K:N.13, K:T.15 LHG.80: 21 residues within 4Å: Chain A: R.140, W.142, V.145, F.273, W.284 Chain C: F.15, W.18, W.425, R.429 Chain D: E.209, N.210, A.219, S.220, T.221, F.222 Ligands: SQD.11, CLA.54, CLA.58, CLA.60, DGD.68, UNL.96 15 PLIP interactions: 5 interactions with chain C, 7 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: C:W.18, C:W.18, C:W.425, A:W.142, A:V.145, A:F.273, A:W.284 Hydrogen bonds: C:R.429, C:R.429, D:N.210, D:A.219, D:T.221 Water bridges: A:R.140, A:R.140 Salt bridges: A:R.140 LHG.84: 22 residues within 4Å: Chain A: S.232, N.234 Chain B: W.4, Y.5, R.6, L.460, F.463, W.467, F.478 Chain D: R.129, Y.131, I.134, W.256, F.259, T.267, M.271 Chain K: L.23, I.24 Ligands: CLA.27, CLA.31, CLA.33, LHG.98 12 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A, 2 interactions with chain K, 2 interactions with chain D Hydrophobic interactions: B:W.4, B:Y.5, B:L.460, K:L.23, K:I.24 Water bridges: B:R.6, B:R.6 Salt bridges: B:R.6 Hydrogen bonds: A:S.232, A:N.234, D:R.129, D:Y.131 LHG.85: 18 residues within 4Å: Chain A: L.258, I.259, F.260, Y.262, A.263 Chain D: F.17, V.18 Chain E: T.4, T.5, G.6, E.7, R.8, P.9, F.10, S.11 Chain F: R.18 Ligands: CLA.6, PL9.16 12 PLIP interactions: 1 interactions with chain A, 10 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: A:A.263, E:F.10 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, E:S.11, F:R.18 LHG.98: 26 residues within 4Å: Chain A: S.232, N.234 Chain B: P.3, W.4, Y.5 Chain D: W.256, F.260, F.263 Chain K: E.11, L.12, N.13, S.16, L.19, G.20, L.23, V.26 Chain L: P.18, F.21 Ligands: CLA.5, CLA.31, CLA.34, BCR.37, LMG.41, PL9.78, LHG.79, LHG.84 15 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L, 4 interactions with chain B, 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: K:V.26, L:P.18, B:W.4, B:W.4, D:W.256, D:F.260, D:F.263 Hydrogen bonds: K:E.11, K:N.13, K:S.16, B:W.4, B:Y.5, A:S.232, A:S.232, A:N.234

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

HEM.87: 20 residues within 4Å: Chain E: R.8, F.10, I.13, R.18, Y.19, I.22, H.23, T.26, I.27, L.30 Chain F: I.14, R.18, W.19, V.22, H.23, A.26, V.27, I.30 Chain T: A.18, I.22 21 PLIP interactions: 11 interactions with chain F, 2 interactions with chain T, 8 interactions with chain E, Hydrophobic interactions: F:I.14, F:W.19, F:V.22, F:A.26, F:V.27, F:I.30, T:A.18, T:I.22, E:I.13, E:T.26, E:I.27, E:I.27 Salt bridges: F:R.18, E:R.8, E:R.18 pi-Stacking: F:W.19, F:W.19, E:Y.19 pi-Cation interactions: F:H.23 Metal complexes: F:H.23, E:H.23

1 x MG: MAGNESIUM ION(Non-covalent)

MG.95: 5 residues within 4Å: Chain I: G.30, A.33, G.34, L.35 Ligands: LMG.93 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:G.30, I:A.33, I:L.35, H2O.22

1 x HEC: HEME C(Covalent)

HEC.106: 23 residues within 4Å: Chain P: A.36, C.37, S.39, C.40, H.41, T.46, T.48, N.49, L.52, D.53, L.54, T.58, L.59, L.72, Y.75, M.76, T.81, Y.82, I.88, H.92, P.93, I.115, I.119 19 PLIP interactions: 19 interactions with chain P, Hydrophobic interactions: P:A.36, P:T.46, P:N.49, P:L.52, P:L.54, P:L.59, P:L.72, P:Y.75, P:Y.75, P:I.88, P:P.93, P:I.115, P:I.119 Hydrogen bonds: P:N.49, 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., Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL. Nature (2017)

Release Date

2017-03-15

Peptides

Photosystem II D1 protein: A
Photosystem II CP47 reaction center protein: B
Photosystem II CP43 chlorophyll 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 X: Q
Photosystem II reaction center protein Ycf12: R
Photosystem II reaction center protein Z: S
Photosystem II protein Y: T

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
X

R
Y

S
Z

T
R

Membrane

We predict this structure to be a membrane protein.
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Photosystem II D1 protein

Photosystem II CP47 reaction center protein

Photosystem II CP43 chlorophyll 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

Photosystem II manganese-stabilizing polypeptide

Photosystem II reaction center protein T

Photosystem II 12 kDa extrinsic protein

Cytochrome c-550

Photosystem II reaction center protein X

Photosystem II reaction center protein Ycf12

Photosystem II reaction center protein Z

Photosystem II protein Y

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