SMTL ID : 5ws6.2 (1 other biounit)

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

Coordinates

PDB Format Compare

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-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.20 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Metal complexes: D:H.204, D:H.258, A:H.215, A:H.272

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.21: 5 residues within 4Å: Chain A: H.337, N.338, F.339 Chain C: G.335, E.336 Ligand excluded by PLIP

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.3: 30 residues within 4Å: Chain A: F.119, Y.147, P.150, L.151, 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, V.283, A.286, A.287, I.290 Chain D: L.172, L.195, F.247 Ligands: CLA.4, PHO.5, CLA.22, CLA.80, LHG.85 17 PLIP interactions: 13 interactions with chain A, 4 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:V.205, A:F.206, A:F.206, A:I.290, D:L.172, D:L.172, D:L.195, D:F.247 Metal complexes: A:H.198 CLA.4: 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.3, PHO.6, PL9.14, LHG.19, DGD.72, CLA.80, LMG.96 13 PLIP interactions: 7 interactions with chain D, 5 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: D:F.147, D:F.147, D:I.168, D:F.169, D:F.171, D:L.172, D:L.172, A:V.202, A:F.206, A:L.210, A:W.278 pi-Stacking: A:F.206 Metal complexes: H2O.5 CLA.7: 27 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 Ligands: BCR.8, LMG.17, CLA.59, CLA.60, BCR.69, DGD.70, UNL.95 19 PLIP interactions: 5 interactions with chain H, 14 interactions with chain A, Hydrophobic interactions: H:V.8, H:V.11, H:F.15, H:F.15, H:V.16, A:I.36, 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 Hydrogen bonds: A:I.96 Salt bridges: A:H.118 Metal complexes: A:H.118 CLA.22: 21 residues within 4Å: Chain A: T.45, 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: CLA.3, PHO.5, SQD.11, CLA.80, PL9.83, LHG.100 7 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: A:T.45, A:V.157, A:F.158, A:F.180, A:F.182, D:L.199 Metal complexes: H2O.2 CLA.24: 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.25, HTG.48, BCR.93 10 PLIP interactions: 5 interactions with chain G, 4 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 Metal complexes: H2O.6 CLA.25: 28 residues within 4Å: Chain B: E.183, 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: V.144, L.152 Chain G: F.37, F.40, I.44, L.45, Y.48 Ligands: CLA.24, CLA.26, CLA.28, CLA.32, BCR.93, DGD.94 20 PLIP interactions: 13 interactions with chain B, 5 interactions with chain G, 2 interactions with chain D, Hydrophobic interactions: B:W.184, B:F.189, B:F.189, B:A.199, B:H.200, B:A.203, B:A.204, B:V.207, B:V.207, B:F.245, B:F.246, B:F.246, G:F.37, G:F.40, G:I.44, G:I.44, D:V.144, D:L.152 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, V.197, H.200, H.201, F.246, A.247, V.250, V.251, T.261 Chain G: M.34, F.37 Ligands: CLA.25, CLA.27, CLA.28, CLA.29, CLA.31, CLA.32, CLA.33 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:L.68, B:A.145, B:L.148, B:L.148, B:F.152, B:F.152, B:F.246, B:F.246, B:F.246, B:A.247, B:V.250 Hydrogen bonds: B:R.67 Salt bridges: B:R.67 pi-Cation interactions: B:H.200 Metal complexes: B:H.201 CLA.27: 22 residues within 4Å: Chain B: W.32, F.60, F.64, R.67, L.144, L.148, V.244, A.247, A.248, V.251, F.450, H.454, F.457, F.461 Ligands: CLA.26, CLA.28, CLA.30, CLA.33, CLA.35, CLA.36, CLA.38, UNL.52 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.32, B:F.60, B:F.64, B:F.64, B:L.144, 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: 30 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.32, 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, 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.26, CLA.28, CLA.39, BCR.42, UNL.52 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:L.68, B:W.90, B:W.90, B:A.98, B:V.101, B:L.102, B:L.148, B:F.155, B:F.161, B:F.161 Metal complexes: B:H.156 CLA.30: 25 residues within 4Å: Chain B: W.32, M.36, Y.39, Q.57, G.58, M.59, F.60, L.323, T.326, G.327, P.328, W.449, F.450, A.453, H.454 Chain D: T.267, M.271 Chain L: F.14 Ligands: CLA.27, CLA.36, BCR.40, BCR.41, LMG.44, PL9.83, LHG.84 12 PLIP interactions: 9 interactions with chain B, 1 interactions with chain L, 1 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.39, B:F.60, B:F.60, B:F.60, B:T.326, B:W.449, B:W.449, L:F.14, D:T.267 Hydrogen bonds: B:G.327 pi-Stacking: B:F.60 Metal complexes: H2O.11 CLA.31: 27 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.26, F.110, I.113, M.116, L.117, F.120, I.140 Chain G: L.42 Ligands: CLA.26, CLA.32, CLA.33, CLA.81, UNL.88, DGD.94 19 PLIP interactions: 10 interactions with chain B, 8 interactions with chain D, 1 interactions with chain G, Hydrophobic interactions: B:A.242, B:F.245, B:F.246, B:F.462, B:F.462, B:I.466, B:L.473, D:L.26, D:F.110, D:F.110, D:I.113, D:M.116, D:L.117, D:F.120, D:I.140, G:L.42 Hydrogen bonds: B:S.238 Water bridges: B:S.239 Metal complexes: B:H.465 CLA.32: 28 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, M.230 Chain D: F.110 Chain G: T.26, T.27, M.30, F.33, M.34, L.41, L.42 Ligands: CLA.25, CLA.26, CLA.28, CLA.31, CLA.33, UNL.88, BCR.93 17 PLIP interactions: 12 interactions with chain B, 4 interactions with chain G, 1 interactions with chain D, Hydrophobic interactions: B:F.138, 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, G:M.30, G:F.33, G:L.41, G:L.42, D:F.110 Salt bridges: B:H.215 Metal complexes: B:H.215 CLA.33: 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.26, CLA.27, CLA.28, CLA.31, CLA.32, CLA.35, CLA.38 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.134, B:M.137, B:F.138, B:L.228, B:M.230, B:I.233, 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, F.478 Chain L: F.21 Ligands: CLA.35, CLA.36, CLA.37, LHG.84, LHG.100 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain L, Hydrophobic interactions: B:W.4, B:W.4, B:H.8, B:T.9, B:L.237, B:L.237, B:I.241, B:I.241, B:F.457, B:F.461, B:F.461, B:F.463, L:F.21 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: 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.27, CLA.28, CLA.33, CLA.34, CLA.36, CLA.37, CLA.38 17 PLIP interactions: 17 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: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.44, LHG.84 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:V.29, B:V.29, B:W.32, B:W.32, B:F.461, B:F.461 Salt bridges: B:H.8 Metal complexes: B:H.25 CLA.37: 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.34, CLA.35, CLA.36, BCR.40, SQD.43, LMG.44, LHG.100 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain L, Hydrophobic interactions: 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: 6 interactions with chain B, 4 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.13, G:L.13 Hydrogen bonds: B:H.22 Metal complexes: B:H.141 CLA.39: 14 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.29, CLA.38, BCR.42 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain G, Hydrophobic interactions: B:I.19, B:L.23, B:A.109, B:W.112, B:W.112, B:L.119, 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:W.5 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.69 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:A.154, 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, C:V.278 Hydrogen bonds: C:Y.279 Metal complexes: C:H.219 CLA.56: 25 residues within 4Å: Chain C: W.45, I.69, H.73, L.77, W.79, L.156, K.160, 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.63, CLA.64, CLA.66, HTG.75 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:W.45, C:W.45, C:I.69, C:L.77, C:W.79, C:L.156, C:L.156, C:K.160, C:F.164, C:L.261, C:M.264, C:A.268, C:L.408, 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: 19 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, M.264 Ligands: CLA.55, CLA.56, CLA.61, CLA.63, CLA.64, CLA.66, CLA.67, LMG.74 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: 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.56, CLA.62, CLA.64, DGD.71, DGD.72, LMG.73, LHG.86 12 PLIP interactions: 10 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:I.69, C:W.407, C:W.407, C:L.408, C:F.418, C:F.418, J:V.21 pi-Stacking: C:W.407 Metal complexes: H2O.16 CLA.59: 24 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, M.263, L.420, H.423, L.424, A.427, R.431 Chain H: V.16, F.19, F.23 Ligands: CLA.7, LMG.17, CLA.61, BCR.69, DGD.70 19 PLIP interactions: 4 interactions with chain H, 10 interactions with chain C, 5 interactions with chain A, Hydrophobic interactions: H:V.16, H:F.19, H:F.19, H:F.23, C:F.246, C:Y.256, C:Y.256, C:L.420, C:L.420, A:F.33, A:W.131, A:W.131, A:W.131 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: 21 residues within 4Å: Chain C: L.143, L.147, L.195, L.196, I.225, C.226, G.229, W.232, H.233, T.236, T.237, P.238, F.239, W.241, A.242, F.246 Ligands: CLA.7, CLA.55, CLA.61, BCR.69, DGD.70 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.147, C:L.147, C:L.195, C:L.195, C:L.196, C:I.225, C:W.232, C:F.246 Hydrogen bonds: C:F.239 Salt bridges: C:H.233 Metal complexes: C:H.233 CLA.61: 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.55, CLA.57, CLA.59, CLA.60, CLA.63, BCR.69 15 PLIP interactions: 14 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:F.246, C:W.248, C:Y.253, C:Y.253, C:Y.256, C:Y.256, C:Y.256, C:L.261 Metal complexes: H2O.13 CLA.62: 25 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, V.421, G.422, W.425, H.426, R.429 Ligands: SQD.9, CLA.58, CLA.63, CLA.64, CLA.65, DGD.71, DGD.72, LMG.73, LHG.86 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:N.21, C:A.22, C:L.254, C:L.254, C:L.258, C:F.419, C:F.419, C:V.421, 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: 24 residues within 4Å: Chain C: N.21, L.24, 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, L.261 Ligands: CLA.56, CLA.57, CLA.61, CLA.62, CLA.64, CLA.65, CLA.66 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:N.21, C:L.24, C:L.31, 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: 19 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, F.23, L.24 Ligands: CLA.56, CLA.57, CLA.58, CLA.62, CLA.63, CLA.65, LHG.86 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain J, Hydrophobic interactions: C:L.41, C:I.42, C:W.45, C:W.45, C:L.261, C:F.418, C:F.419, J:P.20, J:V.21, J:F.23, J:L.24, J:L.24 Hydrogen bonds: C:N.21 Metal complexes: C:H.38 CLA.65: 35 residues within 4Å: Chain C: R.8, W.17, G.20, N.21, R.23, L.24, L.27, K.30, A.34, A.37, H.38, A.105, G.108, F.109, V.112, I.116 Chain J: F.23, L.24, A.27, W.30, Q.31 Chain R: I.20, 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.99, LMG.111 24 PLIP interactions: 9 interactions with chain C, 8 interactions with chain J, 2 interactions with chain R, 5 interactions with chain S, Hydrophobic interactions: C:W.17, C:L.24, C:L.24, C:A.37, C:F.109, C:V.112, J:F.23, J:F.23, J:L.24, J:A.27, J:W.30, J:Q.31, R:I.20, R:L.30, S:V.20, S:V.23, S:P.24, S:P.24, S:A.28 Hydrogen bonds: C:R.23, C:R.23 Salt bridges: C:R.8 pi-Stacking: J:W.30, J:W.30 CLA.66: 18 residues within 4Å: Chain C: L.32, H.35, A.39, L.107, F.128, F.129, F.145, H.146, I.148, V.149, I.152, G.153, L.156 Ligands: CLA.56, CLA.57, CLA.63, CLA.67, BCR.68 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:L.32, C:H.35, C:F.128, C:F.145, C:F.145, C:F.145, C:F.145, C:F.145, C:I.148, C:V.149, C:I.152, C:I.152, C:L.156 Metal complexes: C:H.146 CLA.67: 15 residues within 4Å: Chain C: L.32, V.36, V.106, L.107, G.110, Y.113, H.114, P.119, Y.125, F.129 Ligands: CLA.57, CLA.66, BCR.68, LMG.74, LMG.111 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.32, C:V.36, C:V.106, C:L.107, C:Y.113, C:Y.125, C:F.129 Hydrogen bonds: C:Y.113 Salt bridges: C:H.114 pi-Stacking: C:F.129 Metal complexes: C:H.114 CLA.80: 31 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.3, CLA.4, PHO.6, PL9.14, CLA.22, LMG.96 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.81: 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: G.35, L.36, L.38, L.42 Chain Q: G.12, L.13, G.16, A.17, V.19 Ligands: PL9.14, CLA.31, UNL.88, SQD.91, UNL.109 16 PLIP interactions: 11 interactions with chain D, 2 interactions with chain Q, 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, Q:L.13, Q:V.19, G:L.36, 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.5: 29 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.280, V.283 Chain D: L.195, A.198, L.199, A.202, I.203, W.243, F.247 Ligands: CLA.3, CLA.22, LHG.85 16 PLIP interactions: 14 interactions with chain A, 2 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:Y.147, A:P.150, A:F.158, A:V.205, A:P.279, D:L.195, D:A.202 Hydrogen bonds: A:Q.130, A:Y.147 PHO.6: 31 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.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.4, PL9.14, CLA.80 21 PLIP interactions: 19 interactions with chain D, 2 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:A.135, D:F.136, D:F.136, D:P.139, D:F.143, D:V.165, D:P.265, D:L.269, A:F.206, A:A.209 Hydrogen bonds: D:Q.119, D:N.132

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

BCR.8: 16 residues within 4Å: Chain A: W.20, V.35, L.42, A.43, C.47, I.50, A.51, A.55, I.96, W.105, L.106, P.111 Chain H: F.15 Ligands: CLA.7, UNL.15, UNL.95 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:W.20, A:V.35, A:L.42, A:A.43, A:I.50, A:A.51, A:I.96, A:W.105, A:L.106, A:P.111, H:F.15 BCR.40: 11 residues within 4Å: Chain B: M.24, L.28, C.111, W.114 Chain L: L.13 Ligands: CLA.30, CLA.36, CLA.37, BCR.41, SQD.43, LMG.44 5 PLIP interactions: 1 interactions with chain L, 4 interactions with chain B Hydrophobic interactions: L:L.13, B:L.28, B:L.28, B:W.114, B:W.114 BCR.41: 13 residues within 4Å: Chain B: L.28, G.31, W.32, S.35, I.100, V.101, S.103, G.104 Ligands: CLA.30, CLA.36, BCR.40, SQD.43, LMG.44 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.28, B:W.32, B:I.100 BCR.42: 13 residues within 4Å: Chain B: L.102, L.105, L.106, L.108, A.109, C.111, W.112, V.115 Ligands: CLA.28, CLA.29, CLA.38, CLA.39, UNL.52 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.102, B:L.105, B:L.106, B:V.115 BCR.68: 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.66, CLA.67, LMG.74 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain S Hydrophobic interactions: C:F.94, C:V.98, C:I.102, C:V.106, C:V.106, C:L.107, C:F.129, S:F.59 BCR.69: 20 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.7, CLA.55, CLA.59, CLA.60, CLA.61 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: C:I.191, C:F.192, C:Y.194, C:L.195, C:I.206, C:V.209, C:I.222, C:F.246, H:V.20, H:F.23, H:L.24 BCR.82: 16 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: LMG.96 11 PLIP interactions: 4 interactions with chain D, 5 interactions with chain F, 2 interactions with chain I Hydrophobic interactions: D:Y.32, D:L.39, D:F.91, D:F.103, F:P.28, F:F.32, F:F.32, F:L.33, F:I.36, I:V.20, I:V.24 BCR.93: 16 residues within 4Å: Chain G: M.30, F.33, 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.24, CLA.25, CLA.32 10 PLIP interactions: 2 interactions with chain Q, 8 interactions with chain G Hydrophobic interactions: Q:L.6, Q:F.10, G:F.33, G:F.37, G:F.37, G:F.37, G:F.37, G:V.39, G:F.40, G:L.54 BCR.99: 18 residues within 4Å: Chain C: A.37, G.40, L.41, F.94, L.101, S.104, A.105, G.108, V.112, A.115 Chain J: Y.6, F.9, F.23 Chain S: L.9, V.13, S.16 Ligands: CLA.65, BCR.110 13 PLIP interactions: 6 interactions with chain C, 5 interactions with chain J, 2 interactions with chain S Hydrophobic interactions: C:A.37, C:L.41, C:F.94, C:A.105, C:V.112, C:A.115, J:Y.6, J:Y.6, J:F.9, J:F.23, J:F.23, S:L.9, S:V.13 BCR.105: 10 residues within 4Å: Chain A: L.28 Chain N: F.8, A.11, I.14, A.15, F.17, F.18, I.21, F.22 Ligands: SQD.11 8 PLIP interactions: 7 interactions with chain N, 1 interactions with chain A Hydrophobic interactions: N:A.11, N:I.14, N:A.15, N:F.17, N:F.18, N:F.18, N:F.22, A:L.28 BCR.110: 25 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, A.25, L.26, F.28, V.29, A.32 Chain R: I.12, G.13, G.16, P.17 Chain S: V.13, S.16, F.17, V.20 Ligands: SQD.9, UNL.79, BCR.99 14 PLIP interactions: 10 interactions with chain J, 1 interactions with chain C, 2 interactions with chain R, 1 interactions with chain S Hydrophobic interactions: J:L.12, J:L.16, J:I.19, J:I.19, J:L.22, J:L.22, J:A.25, J:L.26, J:V.29, J:A.32, C:F.44, R:I.12, R:P.17, S:V.20

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

SQD.9: 23 residues within 4Å: Chain A: L.200, A.203, G.204, F.265, N.267, S.270, F.273, W.278, V.281, G.282 Chain C: Q.10, A.16, W.17, W.18 Chain D: S.220, F.222, R.223 Chain J: F.28 Ligands: CLA.62, LMG.73, UNL.79, LHG.86, BCR.110 17 PLIP interactions: 10 interactions with chain A, 1 interactions with chain J, 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: A:A.203, A:F.265, A:F.273, A:W.278, A:W.278, A:V.281, J:F.28, C:W.17, C:W.18 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 Salt bridges: D:R.223 SQD.11: 11 residues within 4Å: Chain A: W.20, N.26, R.27, L.28, I.38, L.42 Chain N: F.22 Ligands: UNL.15, CLA.22, UNL.95, BCR.105 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.26, A:I.38, A:I.38, A:L.42 Hydrogen bonds: A:W.20, A:R.27, A:L.28 SQD.43: 8 residues within 4Å: Chain B: R.17, L.28, S.103, W.114 Chain K: R.7 Ligands: CLA.37, BCR.40, BCR.41 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain K Hydrophobic interactions: B:L.28 Water bridges: B:R.17 Salt bridges: B:R.17, K:R.7 Hydrogen bonds: K:R.7, K:R.7 SQD.91: 13 residues within 4Å: Chain D: R.16 Chain E: E.7 Chain F: I.14, F.15, T.16, V.17, V.20 Chain Q: T.23, V.26, I.30, D.34 Ligands: PL9.14, CLA.81 8 PLIP interactions: 3 interactions with chain Q, 4 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: Q:V.26, Q:I.30, F:F.15, F:F.15 Hydrogen bonds: Q:D.34, F:F.15, F:V.17 Salt bridges: D:R.16

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 1 residues within 4Å: Chain A: D.103 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain A Water bridges: M:Q.107, A:D.103, A:D.103 GOL.16: 10 residues within 4Å: Chain A: G.74, N.75, N.76 Chain D: S.290, Q.291 Chain K: N.37 Chain L: M.1, V.3 Chain N: E.2, Y.6 8 PLIP interactions: 3 interactions with chain N, 1 interactions with chain A, 3 interactions with chain D, 1 interactions with chain K Hydrogen bonds: N:E.2, N:E.2, N:Y.6, D:S.290, D:S.290, D:Q.291 Water bridges: A:G.74, K:N.37 GOL.50: 8 residues within 4Å: Chain B: I.12, N.13, P.130, A.131, L.132, G.231, N.232, I.233 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.13, B:L.132, B:L.132, B:I.233 Water bridges: B:N.232 GOL.54: 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 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain P Hydrogen bonds: C:M.378, C:A.381, C:V.392, C:E.395, P:K.47 Water bridges: C:T.379, C:T.379, C:G.390, P:K.47 GOL.107: 7 residues within 4Å: Chain A: L.341 Chain C: V.392, E.395 Chain O: K.104 Chain P: G.133, K.134, Y.137 3 PLIP interactions: 1 interactions with chain O, 1 interactions with chain P, 1 interactions with chain C Water bridges: O:K.104 Hydrogen bonds: P:K.134, C:E.395

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

OEX.12: 11 residues within 4Å: Chain A: D.61, D.170, E.189, H.332, E.333, H.337, D.342, A.344 Chain C: E.336, R.339 Ligands: OEY.13 18 PLIP interactions: 9 interactions with chain A, 5 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, C:E.336, H2O.1, H2O.2, H2O.2, H2O.4 Hydrogen bonds: C:R.339, C:R.339

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

OEY.13: 12 residues within 4Å: Chain A: D.61, D.170, V.185, E.189, H.332, E.333, H.337, D.342, A.344 Chain C: E.336, R.339 Ligands: OEX.12 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.2, H2O.4 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)

PL9.14: 30 residues within 4Å: Chain A: F.211, M.214, H.215, L.218, I.248, A.251, H.252, F.255, I.259, A.263, S.264, F.265, L.271, F.274 Chain D: V.20, F.28, P.29, L.35 Chain F: V.17, A.21, T.24, L.25 Chain Q: T.23, L.27 Ligands: CLA.4, PHO.6, LHG.19, CLA.80, CLA.81, SQD.91 23 PLIP interactions: 15 interactions with chain A, 5 interactions with chain D, 2 interactions with chain F, 1 interactions with chain Q Hydrophobic interactions: A:F.211, A:F.211, A:M.214, A:L.218, A:I.248, A:A.251, A:H.252, A:F.255, A:F.255, A:I.259, A:F.265, A:L.271, A:L.271, A:F.274, D:V.20, D:F.28, D:F.28, D:P.29, D:L.35, F:V.17, F:L.25, Q:L.27 Hydrogen bonds: A:F.265 PL9.83: 34 residues within 4Å: Chain A: F.52, I.53, I.77, I.176 Chain D: M.188, M.189, A.192, G.193, L.199, I.203, 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.27, L.29 Chain N: F.10 Ligands: CLA.22, CLA.30, LHG.85, LHG.100 25 PLIP interactions: 16 interactions with chain D, 4 interactions with chain A, 3 interactions with chain K, 2 interactions with chain N Hydrophobic interactions: D:M.189, D:A.192, D:L.199, D:I.203, 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:F.52, A:I.53, A:I.77, A:I.176, K:L.23, K:L.27, K:L.29, N:F.10, N:F.10 Hydrogen bonds: D:T.207, D:F.251

9 x UNL: UNKNOWN LIGAND

UNL.15: 6 residues within 4Å: Chain A: R.16, F.17, W.20 Ligands: BCR.8, SQD.11, UNL.95 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.17, A:W.20, A:W.20, A:W.20 Salt bridges: A:R.16 UNL.52: 6 residues within 4Å: Chain B: W.90, L.148 Ligands: CLA.27, CLA.28, CLA.29, BCR.42 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.148 UNL.79: 6 residues within 4Å: Chain C: W.17 Chain J: F.28, F.36 Ligands: SQD.9, LHG.86, BCR.110 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:W.17, C:W.17, J:F.28, J:F.36, J:F.36 UNL.87: 5 residues within 4Å: Chain D: W.22, S.23, I.25 Chain Q: L.20 Ligands: UNL.88 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain Q Hydrophobic interactions: D:I.25, Q:L.20 UNL.88: 10 residues within 4Å: Chain B: A.227, R.229 Chain D: D.9, K.13, W.22 Ligands: CLA.31, CLA.32, LMT.45, CLA.81, UNL.87 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:A.227 Hydrogen bonds: B:R.229, B:R.229 Salt bridges: D:K.13 UNL.95: 8 residues within 4Å: Chain H: M.1, T.3, L.4, T.7 Ligands: CLA.7, BCR.8, SQD.11, UNL.15 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:L.4, H:L.4, H:T.7 Hydrogen bonds: H:T.3 UNL.97: 3 residues within 4Å: Chain I: G.25 Ligands: DGD.71, LMG.73 No protein-ligand interaction detected (PLIP) UNL.101: 1 residues within 4Å: Chain L: I.23 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:I.23 UNL.109: 8 residues within 4Å: Chain D: L.82, W.83, G.89 Chain Q: S.15, G.16, V.19, L.20 Ligands: CLA.81 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain Q Hydrophobic interactions: D:L.82, D:W.83, Q:V.19, Q:L.20

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

LMG.17: 18 residues within 4Å: Chain A: F.93, W.97, E.98, F.117, L.120, F.155 Chain C: L.195, L.196, S.198, F.200, W.205, F.266, L.420 Chain H: K.5, Y.9 Ligands: CLA.7, CLA.59, DGD.70 17 PLIP interactions: 7 interactions with chain C, 6 interactions with chain A, 4 interactions with chain H Hydrophobic interactions: C:W.205, C:W.205, C:F.266, C:F.266, C:L.420, A:F.117, A:F.117, A:L.120, A:F.155 Hydrogen bonds: C:E.203, A:W.97, A:E.98, H:K.5, H:K.5, H:Y.9, H:Y.9 Water bridges: C:S.198 LMG.44: 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, F.14 Ligands: CLA.30, CLA.36, CLA.37, BCR.40, BCR.41, LHG.84, LHG.100 10 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K, 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: L:A.10, K:F.35, B:F.452, B:V.456, D:I.274 Hydrogen bonds: L:N.4, B:T.326, B:T.326 Water bridges: L:N.4, B:T.326 LMG.73: 12 residues within 4Å: Chain C: F.52, H.56 Chain I: I.21 Chain J: D.14, V.18, V.21 Chain R: Q.5 Ligands: SQD.9, CLA.58, CLA.62, DGD.71, UNL.97 7 PLIP interactions: 3 interactions with chain J, 1 interactions with chain R, 2 interactions with chain C, 1 interactions with chain I Hydrophobic interactions: J:V.18, J:V.18, J:V.21, I:I.21 Hydrogen bonds: R:Q.5 Water bridges: C:H.56 Salt bridges: C:H.56 LMG.74: 15 residues within 4Å: Chain C: V.43, W.79, D.89, F.91, V.95, V.96, V.99, H.100, S.103 Chain S: F.59, V.62 Ligands: CLA.57, CLA.67, BCR.68, HTG.75 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.43, C:V.96, C:V.99 Hydrogen bonds: C:D.89 LMG.96: 20 residues within 4Å: Chain D: L.39, 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.4, DGD.72, CLA.80, BCR.82, MG.98 12 PLIP interactions: 6 interactions with chain D, 3 interactions with chain I, 3 interactions with chain F Hydrophobic interactions: D:L.39, D:F.63, D:F.63, D:F.63 Hydrogen bonds: D:F.63, I:G.30, F:M.39, F:Q.40 Water bridges: D:N.62, I:F.27, I:G.36, F:I.42 LMG.111: 12 residues within 4Å: Chain C: F.109, Y.113, R.117 Chain S: M.19, Y.27, W.33, K.37, F.41, S.44, W.47 Ligands: CLA.65, CLA.67 10 PLIP interactions: 5 interactions with chain S, 5 interactions with chain C Hydrophobic interactions: S:M.19, S:F.41, S:W.47, C:F.109, C:F.109 Salt bridges: S:K.37, S:K.37 Hydrogen bonds: C:Y.113, C:R.117, C:R.117

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

LMT.18: 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 8 PLIP interactions: 3 interactions with chain C, 4 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: C:W.241, H:L.24 Hydrogen bonds: C:R.244, C:R.244, H:S.25, H:R.30, A:N.12 Water bridges: H:R.30 LMT.23: 5 residues within 4Å: Chain A: I.53, L.72, Y.73 Chain D: R.294 Chain M: G.110 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain M, 2 interactions with chain D Hydrophobic interactions: A:I.53, A:L.72 Hydrogen bonds: A:Y.73, M:G.110, D:R.294, D:R.294 LMT.45: 13 residues within 4Å: Chain B: R.223, L.224, K.226, A.227, K.497, D.500 Chain D: F.5, D.6, D.9 Chain G: W.24, M.30, M.34 Ligands: UNL.88 10 PLIP interactions: 6 interactions with chain B, 2 interactions with chain D, 2 interactions with chain G Hydrophobic interactions: B:L.224, B:A.227, D:F.5, G:W.24, G:W.24 Hydrogen bonds: B:R.223, B:K.226, D:D.6 Salt bridges: B:R.223, B:K.226 LMT.53: 1 residues within 4Å: Chain B: A.42 No protein-ligand interaction detected (PLIP) LMT.89: 6 residues within 4Å: Chain E: F.31, W.35, S.39 Chain F: F.41, I.42, Q.43 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:F.31, E:W.35, F:F.41 Hydrogen bonds: E:S.39, E:S.39, F:Q.43 Water bridges: F:Q.43 LMT.102: 6 residues within 4Å: Chain L: V.27, E.30, S.31, Q.32, Q.33, K.34 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:E.30, L:Q.32, L:Q.33, L:K.34 LMT.104: 5 residues within 4Å: Chain L: L.8, A.12 Chain N: M.1, I.4, F.8 5 PLIP interactions: 3 interactions with chain N, 2 interactions with chain L Hydrophobic interactions: N:I.4, N:F.8, N:F.8, L:L.8, L:A.12

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

LHG.19: 11 residues within 4Å: Chain A: I.259, F.260, Y.262 Chain D: F.17 Chain E: E.7, P.9, F.10, S.11 Chain F: R.18 Ligands: CLA.4, PL9.14 8 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: A:I.259, A:F.260, A:F.260, A:F.260 Hydrogen bonds: F:R.18, E:E.7, E:F.10, E:S.11 LHG.84: 24 residues within 4Å: Chain A: 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, F.263, T.267, M.271 Chain K: L.23 Chain L: F.14, P.18 Ligands: CLA.30, CLA.34, CLA.36, LMG.44, LHG.100 15 PLIP interactions: 6 interactions with chain B, 2 interactions with chain L, 4 interactions with chain D, 2 interactions with chain A, 1 interactions with chain K Hydrophobic interactions: B:W.4, B:Y.5, B:L.460, L:F.14, L:P.18, D:F.263, K:L.23 Water bridges: B:R.6, B:R.6, D:R.129 Salt bridges: B:R.6 Hydrogen bonds: D:R.129, D:Y.131, A:N.234, A:N.234 LHG.85: 23 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.29 Chain N: F.17, A.20, I.21 Ligands: CLA.3, PHO.5, PL9.83, LHG.100 17 PLIP interactions: 5 interactions with chain N, 8 interactions with chain D, 4 interactions with chain K Hydrophobic interactions: N:F.17, N:F.17, N:F.17, N:A.20, N:I.21, D:F.247, D:I.249, D:F.251, D:F.260, D:F.260, K:Y.18, K:L.29 Hydrogen bonds: D:S.252, D:S.252, D:N.253, K:N.13, K:N.13 LHG.86: 19 residues within 4Å: Chain A: R.140, W.142, F.273, V.280 Chain C: W.18, W.425, R.429 Chain D: E.209, N.210, A.219, S.220, T.221, F.222 Ligands: SQD.9, CLA.58, CLA.62, CLA.64, DGD.72, UNL.79 13 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: C:W.18, C:W.18, C:W.425, A:F.273, A:F.273, A:V.280 Hydrogen bonds: C:R.429, C:R.429, D:N.210, D:A.219, D:T.221 Salt bridges: A:R.140, A:R.140 LHG.100: 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.22, L.23 Chain L: V.17, P.18, F.21 Ligands: CLA.22, CLA.34, CLA.37, LMG.44, PL9.83, LHG.84, LHG.85 13 PLIP interactions: 4 interactions with chain K, 2 interactions with chain B, 3 interactions with chain A, 3 interactions with chain D, 1 interactions with chain L Hydrophobic interactions: K:L.23, D:F.260, D:F.263, D:F.263, L:V.17 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 BCT: BICARBONATE ION(Non-functional Binders)

BCT.20: 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: FE2.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:H.215, D:K.254

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

HTG.46: 5 residues within 4Å: Chain B: S.73, S.75, W.77, E.93, L.97 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.97 Hydrogen bonds: B:S.73, B:E.93 Water bridges: B:L.41 HTG.47: 12 residues within 4Å: Chain B: K.340, S.418, Y.419, K.422, E.430, F.431, T.433 Chain M: Q.174, A.175, K.176, E.177, E.178 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain M Hydrophobic interactions: B:Y.419 Hydrogen bonds: B:K.340, B:K.340, B:F.431, B:F.431, M:Q.174, M:K.176 Water bridges: B:E.430, B:E.430 HTG.48: 3 residues within 4Å: Chain B: W.184, I.206 Ligands: CLA.24 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.184, B:I.206, B:I.206 Hydrogen bonds: B:W.184 HTG.51: 4 residues within 4Å: Chain B: W.74, D.86, G.88, F.89 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.86, B:G.88, B:G.88 HTG.75: 6 residues within 4Å: Chain C: W.79, F.163, F.164, G.165 Ligands: CLA.56, LMG.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.79 HTG.78: 5 residues within 4Å: Chain C: F.163, N.183, P.184, L.186, I.220 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.163, C:I.220 Hydrogen bonds: C:N.183 HTG.92: 6 residues within 4Å: Chain D: G.3, W.4, F.5, D.6 Chain G: W.24, P.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.5

5 x CA: CALCIUM ION(Non-covalent)

CA.49: 2 residues within 4Å: Chain B: N.437 Chain M: E.179 No protein-ligand interaction detected (PLIP) CA.76: 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:T.140, C:T.141, C:H.233, C:I.234, C:T.236 CA.77: 5 residues within 4Å: Chain C: F.4, T.6, D.9, E.11, S.12 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:F.4, C:T.6, C:D.9, C:E.11, C:S.12 CA.103: 3 residues within 4Å: Chain M: T.136, 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.23 CA.106: 2 residues within 4Å: Chain F: R.44 Chain P: E.23 No protein-ligand interaction detected (PLIP)

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

DGD.70: 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, M.263, C.270, F.274, N.275, N.276, T.277, D.342, F.343, R.344, L.420 Ligands: CLA.7, LMG.17, CLA.59, CLA.60 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain C Hydrophobic interactions: A:L.151, A:F.155, A:F.155, A:I.163, C:F.200, C:W.205, C:V.207 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:P.199, C:F.200 DGD.71: 20 residues within 4Å: Chain A: H.195, F.197 Chain C: E.65, Q.66, G.67, L.386, S.388, N.400, F.401, V.402, W.407, T.410, S.411 Chain I: F.28, Y.32 Ligands: CLA.58, CLA.62, DGD.72, LMG.73, UNL.97 14 PLIP interactions: 9 interactions with chain C, 3 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: C:L.386, I:F.28, I:F.28, A:F.197, A:F.197 Hydrogen bonds: C:S.388, C:N.400, C:N.400, C:V.402, C:V.402 Water bridges: C:Q.66, C:G.67, C:G.67, I:Y.32 DGD.72: 28 residues within 4Å: Chain A: Q.199, L.200, A.203, 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 Chain I: F.28, A.31, Y.32, G.36, S.37, S.38 Chain P: Q.34 Ligands: CLA.4, CLA.58, CLA.62, DGD.71, LHG.86, LMG.96 14 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A, 2 interactions with chain P, 4 interactions with chain I Hydrogen bonds: C:N.387, C:N.397, C:S.398, A:S.305, P:Q.34, P:Q.34, I:G.36, I:S.38 Water bridges: C:N.397, I:G.36, I:S.38 Hydrophobic interactions: A:L.200, A:L.200, A:A.203 DGD.94: 28 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, L.106, F.110, I.113, V.144, I.149, L.152, G.153, S.155, L.281 Chain G: L.45, Y.48, N.49, V.59, S.60, W.61 Ligands: CLA.25, CLA.31 22 PLIP interactions: 9 interactions with chain D, 7 interactions with chain G, 6 interactions with chain B Hydrophobic interactions: D:L.106, D:F.110, D:I.113, D:V.144, D:I.149, D:L.152, D:L.281, G:Y.48, G:Y.48, G:Y.48, B:F.249, B:Y.257, B:F.462, 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:Q.273

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

HEM.90: 17 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: R.18, W.19, V.22, H.23, A.26, V.27, I.30 18 PLIP interactions: 10 interactions with chain E, 8 interactions with chain F, Hydrophobic interactions: E:F.10, E:I.13, E:I.22, E:T.26, E:I.27, E:I.27, F:V.22, F:A.26, F:V.27, F:I.30 Hydrogen bonds: E:R.8 Salt bridges: E:R.18, F:R.18 pi-Stacking: E:Y.19, F:W.19 Metal complexes: E:H.23, F:H.23 pi-Cation interactions: F:H.23

1 x MG: MAGNESIUM ION(Non-covalent)

MG.98: 5 residues within 4Å: Chain I: G.30, A.33, G.34, L.35 Ligands: LMG.96 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.108: 21 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, L.72, Y.75, M.76, 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: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:D.53, P:D.53, P:Y.82 Water bridges: P:N.49 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

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

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

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