SMTL ID : 6wj6.1

Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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.214, H.268 Ligands: BCT.55 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Metal complexes: D:H.214, D:H.268, A:H.215, A:H.272

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.2: 31 residues within 4Å: Chain A: F.119, Y.147, P.150, A.153, A.154, 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, I.283, T.286, A.287, V.290 Chain D: I.182, L.183, L.205 Chain L: L.17 Ligands: CLA.3, PHO.4, CLA.53, CLA.56, LHG.61 22 PLIP interactions: 18 interactions with chain A, 1 interactions with chain L, 3 interactions with chain D, Hydrophobic interactions: A:F.119, A:F.119, A:Y.147, A:P.150, A:A.153, A:F.182, A:F.186, A:Q.187, A:I.192, A:I.192, A:L.193, A:L.193, A:V.202, A:V.205, A:I.283, L:L.17, D:I.182, D:L.183, D:L.205 pi-Stacking: A:H.198, A:H.198 Metal complexes: A:H.198 CLA.3: 17 residues within 4Å: Chain A: M.199, V.202, A.203, F.206, G.207, L.210, F.211, W.278 Chain D: L.74, F.157, V.175, I.178, F.179, I.182 Ligands: CLA.2, PHO.54, CLA.56 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain D, Hydrophobic interactions: A:V.202, A:L.210, A:F.211, A:W.278, D:F.157, D:F.157, D:I.178, D:F.179, D:I.182, D:I.182 CLA.5: 21 residues within 4Å: Chain A: L.36, P.39, T.40, T.43, F.93, Y.94, P.95, I.96, W.97, Q.113, L.114, H.118, I.121 Chain H: V.8, Y.9, V.11, V.12, F.15 Ligands: BCR.6, LMG.33, CLA.38 20 PLIP interactions: 8 interactions with chain H, 12 interactions with chain A, Hydrophobic interactions: H:Y.9, H:Y.9, H:V.11, H:V.12, H:V.12, H:F.15, H:F.15, A:L.36, A:T.40, A:F.93, A:P.95, A:I.96, A:W.97, A:W.97 Hydrogen bonds: H:Y.9, A:I.96 Salt bridges: A:H.118 pi-Stacking: A:H.118, A:H.118 Metal complexes: A:H.118 CLA.10: 9 residues within 4Å: Chain B: W.185, G.186, P.187, F.190, A.204 Chain G: F.41, L.55 Ligands: CLA.11, BCR.73 8 PLIP interactions: 4 interactions with chain B, 3 interactions with chain G, 1 Ligand-Water interactions, Hydrophobic interactions: B:P.187, B:F.190, B:F.190, B:A.204, G:F.41, G:F.41, G:L.55 Metal complexes: H2O.3 CLA.11: 26 residues within 4Å: Chain B: W.185, G.189, F.190, G.197, A.200, H.201, A.204, A.205, V.208, F.247, F.250, V.251, T.255, N.260 Chain D: M.159 Chain G: F.38, F.41, I.45, L.46, Y.49 Ligands: CLA.10, CLA.12, CLA.14, CLA.18, DGD.65, BCR.73 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain G, Hydrophobic interactions: B:W.185, B:F.190, B:F.190, B:A.200, B:H.201, B:A.205, B:V.208, B:V.208, B:F.247, B:F.250, G:F.38, G:F.41, G:I.45 Hydrogen bonds: B:N.260 pi-Stacking: B:H.201 Metal complexes: B:H.201 CLA.12: 25 residues within 4Å: Chain B: R.68, L.69, S.146, L.149, C.150, F.153, M.166, V.198, H.201, H.202, A.244, F.247, A.248, V.251, V.252, T.262 Chain G: F.38, L.39 Ligands: CLA.11, CLA.13, CLA.14, CLA.15, CLA.17, CLA.19, BCR.73 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain G, Hydrophobic interactions: B:L.69, B:L.149, B:L.149, B:F.153, B:F.153, B:A.244, B:F.247, B:A.248, B:V.251, B:T.262, G:F.38, G:F.38, G:L.39 Hydrogen bonds: B:R.68 Salt bridges: B:R.68, B:H.202 pi-Stacking: B:H.202 pi-Cation interactions: B:H.201 Metal complexes: B:H.202 CLA.13: 26 residues within 4Å: Chain B: W.33, F.61, F.65, R.68, L.145, L.148, L.149, A.248, A.249, V.252, F.451, H.455, F.458, A.459, F.462 Ligands: CLA.12, CLA.14, CLA.16, CLA.19, CLA.20, CLA.21, CLA.22, CLA.24, BCR.27, LMT.31, LMT.32 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.33, B:F.61, B:F.65, B:L.148, B:L.149, B:L.149, B:A.248, B:V.252, B:V.252, B:F.458, B:F.458, B:F.458, B:F.462, B:F.462 Salt bridges: B:R.68 pi-Stacking: B:F.451, B:F.451, B:H.455 Metal complexes: B:H.455 CLA.14: 29 residues within 4Å: Chain B: T.27, V.30, A.31, W.33, A.34, A.38, V.62, F.65, M.66, R.68, L.69, V.96, H.100, L.103, L.143, S.146, G.147, A.205, G.209 Ligands: CLA.11, CLA.12, CLA.13, CLA.15, CLA.18, CLA.19, CLA.21, CLA.24, BCR.28, LMT.31 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:T.27, B:V.30, B:A.31, B:W.33, B:A.34, B:V.96, B:L.103, B:L.143 Salt bridges: B:R.68 pi-Stacking: B:H.100, B:H.100 Metal complexes: B:H.100 CLA.15: 20 residues within 4Å: Chain B: L.69, G.70, V.71, F.90, W.91, V.96, A.99, H.100, L.103, G.152, F.153, F.156, H.157, W.162, P.164 Ligands: CLA.12, CLA.14, BCR.28, LMT.31, LMT.32 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.69, B:L.69, B:V.71, B:F.90, B:F.90, B:W.91, B:L.103, B:L.103, B:F.153, B:F.156, B:W.162, B:W.162 pi-Stacking: B:H.157 pi-Cation interactions: B:H.157 CLA.16: 28 residues within 4Å: Chain B: W.33, M.37, Y.40, I.44, Q.58, G.59, M.60, F.61, L.324, T.327, G.328, A.329, P.447, W.450, F.451, H.455 Chain D: M.281 Chain J: L.29, F.33, F.37 Chain K: F.14 Ligands: CLA.13, CLA.22, BCR.26, BCR.27, LMG.30, PL9.59, LHG.60 11 PLIP interactions: 7 interactions with chain B, 1 interactions with chain K, 2 interactions with chain J, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.40, B:F.61, B:F.61, B:W.450, B:W.450, K:F.14, J:F.33, J:F.37 Hydrogen bonds: B:G.328 pi-Stacking: B:F.61 Metal complexes: H2O.5 CLA.17: 27 residues within 4Å: Chain B: L.229, T.236, S.239, S.240, A.243, F.246, F.247, F.463, H.466, T.473, L.474 Chain D: L.36, L.89, L.116, F.120, I.123, M.126, L.127, F.130 Chain G: L.43, L.46 Ligands: CLA.12, CLA.18, CLA.19, SQD.29, CLA.57, DGD.65 21 PLIP interactions: 9 interactions with chain D, 11 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: D:L.36, D:L.89, D:L.116, D:F.120, D:I.123, D:I.123, D:M.126, D:L.127, D:F.130, B:A.243, B:F.246, B:F.246, B:F.247, B:F.463, B:F.463, B:L.474, G:L.46 Salt bridges: B:H.466 pi-Stacking: B:H.466 pi-Cation interactions: B:H.466 Metal complexes: B:H.466 CLA.18: 24 residues within 4Å: Chain B: F.139, L.143, V.208, A.212, F.215, H.216, V.219, P.221, P.222, L.225, L.229, M.231 Chain D: F.120 Chain G: T.27, M.31, F.34, L.39, L.42 Ligands: CLA.11, CLA.14, CLA.17, CLA.19, SQD.29, BCR.73 18 PLIP interactions: 13 interactions with chain B, 4 interactions with chain G, 1 interactions with chain D, Hydrophobic interactions: B:F.139, B:F.139, B:L.143, B:V.208, B:A.212, B:F.215, B:F.215, B:L.225, B:L.229, G:M.31, G:F.34, G:L.39, G:L.42, D:F.120 Salt bridges: B:H.216 pi-Stacking: B:H.216, B:H.216 Metal complexes: B:H.216 CLA.19: 23 residues within 4Å: Chain B: H.23, L.135, M.138, F.139, H.142, L.143, L.145, S.146, L.229, M.231, I.234, T.236, V.237, S.240, S.241, A.244 Ligands: CLA.12, CLA.13, CLA.14, CLA.17, CLA.18, CLA.21, CLA.24 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.135, B:M.138, B:F.139, B:H.142, B:L.145, B:L.229, B:M.231, B:I.234, B:T.236, B:V.237, B:A.244 Hydrogen bonds: B:H.142 Metal complexes: H2O.4 CLA.20: 22 residues within 4Å: Chain B: W.5, Y.6, R.7, V.8, H.9, T.10, L.238, I.242, L.461, F.462, F.464, G.465, W.468, H.469, R.472 Ligands: CLA.13, CLA.21, CLA.22, CLA.23, BCR.27, LHG.60, LHG.67 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:W.5, B:W.5, B:H.9, B:T.10, B:L.238, B:L.238, B:F.462, B:F.462, B:F.464, B:W.468 Hydrogen bonds: B:H.9 Salt bridges: B:H.9, B:R.472 pi-Stacking: B:W.468, B:H.469, B:H.469 Metal complexes: B:H.469 CLA.21: 20 residues within 4Å: Chain B: H.9, V.12, L.13, L.19, V.22, H.23, H.26, T.27, I.234, V.237, L.238, S.241, I.242 Ligands: CLA.13, CLA.14, CLA.19, CLA.20, CLA.22, CLA.23, CLA.24 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:V.12, B:L.13, B:L.19, B:V.22, B:H.26, B:I.234, B:V.237, B:L.238 Hydrogen bonds: B:S.241 Salt bridges: B:H.23 pi-Stacking: B:H.26 pi-Cation interactions: B:H.23, B:H.23 Metal complexes: B:H.23 CLA.22: 15 residues within 4Å: Chain B: H.9, H.26, V.30, W.33, L.461, F.462 Ligands: CLA.13, CLA.16, CLA.20, CLA.21, CLA.23, BCR.26, BCR.27, LHG.60, LHG.67 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:V.30, B:V.30, B:W.33, B:W.33, B:L.461, B:L.461, B:F.462, B:F.462 Salt bridges: B:H.9, B:H.9 Metal complexes: B:H.26 CLA.23: 16 residues within 4Å: Chain B: L.3, V.8, H.9, V.11, V.22, M.25, L.29, W.115 Chain J: Q.10, V.12 Chain K: F.21, L.25 Ligands: CLA.20, CLA.21, CLA.22, BCR.26 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain K, Hydrophobic interactions: B:V.8, B:M.25, B:L.29, B:W.115, K:F.21, K:F.21, K:L.25 pi-Stacking: B:H.9, B:H.9 Metal complexes: B:H.9 CLA.24: 20 residues within 4Å: Chain B: I.20, H.23, L.24, T.27, F.123, L.133, M.138, I.141, H.142, L.145 Chain G: L.7, L.11, L.14, N.15 Ligands: CLA.13, CLA.14, CLA.19, CLA.21, CLA.25, BCR.28 12 PLIP interactions: 3 interactions with chain G, 9 interactions with chain B, Hydrophobic interactions: G:L.7, G:L.11, G:L.14, B:I.20, B:F.123, B:L.133, B:I.141, B:I.141, B:L.145 Hydrogen bonds: B:H.23 pi-Stacking: B:H.142 Metal complexes: B:H.142 CLA.25: 15 residues within 4Å: Chain B: I.20, L.24, L.107, A.110, W.113, H.114, L.120, L.122, F.123 Chain G: T.5, L.7, G.8, L.11 Ligands: CLA.24, BCR.28 16 PLIP interactions: 3 interactions with chain G, 13 interactions with chain B, Hydrophobic interactions: G:L.7, G:L.11, B:I.20, B:I.20, B:L.24, B:L.107, B:A.110, B:W.113, B:W.113, B:L.120, B:L.122, B:F.123 Hydrogen bonds: G:T.5 pi-Stacking: B:W.113, B:W.113 Metal complexes: B:H.114 CLA.34: 23 residues within 4Å: Chain C: T.81, L.82, L.155, G.158, A.159, L.162, V.172, I.211, I.220, H.224, I.227, A.265, L.268, M.269, I.272, F.276, A.283, Y.284 Ligands: CLA.35, CLA.36, CLA.39, CLA.40, BCR.48 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:A.159, C:L.162, C:I.211, C:I.227, C:A.265, C:L.268, C:I.272, C:F.276, C:A.283 Hydrogen bonds: C:Y.284 pi-Stacking: C:H.224, C:H.224 Metal complexes: C:H.224 CLA.35: 24 residues within 4Å: Chain C: W.50, L.75, H.78, L.82, W.84, L.161, K.165, L.266, M.269, G.270, A.273, Y.284, L.413, H.417, L.420, G.421, F.424 Ligands: CLA.34, CLA.36, CLA.37, CLA.42, CLA.43, CLA.45, SQD.50 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:W.50, C:L.75, C:L.82, C:W.84, C:L.161, C:L.266, C:M.269, C:A.273, C:L.413, C:L.420, C:F.424 Hydrogen bonds: C:Y.284 Salt bridges: C:H.78, C:H.417 pi-Stacking: C:H.417 Metal complexes: C:H.417 CLA.36: 20 residues within 4Å: Chain C: I.47, V.48, W.50, A.51, T.55, L.75, H.78, I.79, L.82, W.84, V.101, H.105, L.266, M.269 Ligands: CLA.34, CLA.35, CLA.42, CLA.43, CLA.45, SQD.50 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:V.48, C:A.51, C:L.82, C:W.84, C:V.101, C:L.266 Salt bridges: C:H.105 pi-Stacking: C:H.105, C:H.105 CLA.37: 19 residues within 4Å: Chain A: F.285 Chain C: W.50, M.54, F.57, Q.71, G.72, L.73, I.74, W.412, L.413, S.416, H.417, F.423 Chain I: P.25, V.26, L.29 Ligands: CLA.35, CLA.43, LHG.62 14 PLIP interactions: 1 interactions with chain A, 11 interactions with chain C, 1 interactions with chain I, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.285, C:W.50, C:F.57, C:I.74, C:W.412, C:W.412, C:W.412, C:L.413, C:F.423, C:F.423, C:F.423, I:L.29 pi-Stacking: C:W.412 Metal complexes: H2O.6 CLA.38: 25 residues within 4Å: Chain A: F.33, L.36, I.121, F.124, M.127, G.128, W.131 Chain C: L.251, I.252, S.260, Y.261, G.264, L.425, H.428, L.429, A.432, R.436 Chain H: I.16, F.19, F.23 Ligands: CLA.5, LMG.33, CLA.40, BCR.48, DGD.49 19 PLIP interactions: 7 interactions with chain C, 9 interactions with chain A, 3 interactions with chain H, Hydrophobic interactions: C:Y.261, C:Y.261, C:L.425, C:L.429, A:F.33, A:F.33, A:F.33, A:L.36, A:F.124, A:W.131, A:W.131, A:W.131, H:I.16, H:F.19, H:F.23 Hydrogen bonds: C:Y.261 Salt bridges: C:R.436 Metal complexes: C:H.428 pi-Stacking: A:W.131 CLA.39: 20 residues within 4Å: Chain C: I.148, L.152, L.200, W.210, I.230, C.231, G.234, W.237, H.238, T.241, K.242, P.243, F.244, W.246, A.247, L.251 Ligands: LMG.33, CLA.34, CLA.40, BCR.48 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:I.148, C:I.148, C:L.152, C:L.152, C:W.210, C:W.246, C:W.246, C:A.247, C:L.251 Hydrogen bonds: C:F.244 pi-Stacking: C:H.238, C:H.238 Metal complexes: C:H.238 CLA.40: 21 residues within 4Å: Chain C: M.144, T.145, I.147, I.148, H.151, L.152, L.155, I.227, C.231, L.251, W.253, Y.258, Y.261, S.262, A.265, M.269 Ligands: CLA.34, CLA.38, CLA.39, CLA.42, BCR.48 17 PLIP interactions: 16 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:M.144, C:T.145, C:I.147, C:I.148, C:I.148, C:L.155, C:I.227, C:L.251, C:W.253, C:Y.258, C:Y.258, C:Y.261, C:Y.261, C:Y.261, C:A.265 Salt bridges: C:H.151 Metal complexes: H2O.5 CLA.41: 20 residues within 4Å: Chain C: F.20, W.23, S.24, G.25, N.26, A.27, L.259, L.263, F.423, F.424, V.426, G.427, W.430, H.431, R.434 Chain I: F.36 Ligands: CLA.42, CLA.43, CLA.44, LHG.62 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain I, Hydrophobic interactions: C:F.424, C:V.426, C:W.430, C:W.430, I:F.36 Hydrogen bonds: C:N.26, C:N.26 Salt bridges: C:H.431, C:R.434 pi-Stacking: C:W.430, C:H.431, C:H.431 Metal complexes: C:H.431 CLA.42: 24 residues within 4Å: Chain C: N.26, I.30, L.36, A.39, H.40, H.43, I.47, W.138, I.147, H.151, G.255, E.256, Y.258, L.259, S.262, L.263, L.266 Ligands: CLA.35, CLA.36, CLA.40, CLA.41, CLA.43, CLA.44, CLA.45 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:N.26, C:L.36, C:A.39, C:H.43, C:W.138, C:W.138, C:I.147, C:Y.258, C:L.259 Hydrogen bonds: C:S.262 pi-Stacking: C:H.43 pi-Cation interactions: C:H.40 Metal complexes: C:H.40 CLA.43: 15 residues within 4Å: Chain C: N.26, H.43, L.46, I.47, W.50, L.266, F.424 Chain I: P.28, L.32 Ligands: CLA.35, CLA.36, CLA.37, CLA.41, CLA.42, CLA.44 14 PLIP interactions: 2 interactions with chain I, 12 interactions with chain C, Hydrophobic interactions: I:P.28, I:L.32, C:L.46, C:I.47, C:I.47, C:I.47, C:W.50, C:L.266, C:F.424, C:F.424 Hydrogen bonds: C:N.26 pi-Stacking: C:H.43, C:H.43 Metal complexes: C:H.43 CLA.44: 17 residues within 4Å: Chain C: W.22, G.25, N.26, R.28, L.29, L.32, K.35, A.39, L.46, A.120, L.121 Chain I: W.38, Q.39 Ligands: CLA.41, CLA.42, CLA.43, BCR.51 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:W.22, C:L.29, C:L.29, C:K.35, C:L.46, C:A.120 Hydrogen bonds: C:R.28 CLA.45: 18 residues within 4Å: Chain C: H.40, V.41, A.44, L.112, F.133, F.134, Y.136, I.147, Y.150, H.151, L.154, G.158, L.161 Ligands: CLA.35, CLA.36, CLA.42, CLA.46, SQD.50 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:H.40, C:F.133, C:F.134, C:Y.136, C:I.147, C:Y.150, C:Y.150, C:L.154, C:L.154 pi-Stacking: C:H.151 Metal complexes: C:H.151 CLA.46: 16 residues within 4Å: Chain C: L.37, V.41, V.111, L.112, L.114, G.115, Y.118, H.119, P.124, L.127, Y.130, F.134, L.154 Ligands: CLA.45, BCR.47, SQD.50 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:V.41, C:V.41, C:V.111, C:L.112, C:L.114, C:Y.118, C:L.127, C:Y.130, C:F.134, C:L.154 Hydrogen bonds: C:Y.118 Salt bridges: C:H.119 pi-Stacking: C:H.119, C:H.119, C:F.134 Metal complexes: C:H.119 CLA.53: 24 residues within 4Å: Chain A: T.45, F.48, F.119, V.157, F.158, M.172, I.176, T.179, F.180, F.182, M.183 Chain D: M.198, V.201, A.202, L.205, G.206 Chain J: L.32 Ligands: CLA.2, PHO.4, SQD.9, CLA.56, PL9.59, LHG.61, LHG.67 9 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.48, A:F.119, A:V.157, A:F.158, A:T.179, A:F.180, A:F.182, D:V.201 Metal complexes: H2O.1 CLA.56: 28 residues within 4Å: Chain A: M.183, F.206 Chain D: L.45, W.48, L.122, P.149, V.152, S.155, V.156, F.181, I.182, L.185, Q.186, W.191, T.192, H.197, G.200, V.201, I.204, L.205, L.279, S.282, S.283, I.286 Ligands: CLA.2, CLA.3, CLA.53, PHO.54 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain A, Hydrophobic interactions: D:L.45, D:W.48, D:L.122, D:P.149, D:F.181, D:I.182, D:L.185, D:Q.186, D:W.191, D:T.192, D:V.201, D:I.204, D:L.205, D:L.205, A:F.206, A:F.206 pi-Stacking: D:W.191 pi-Cation interactions: D:H.197 Metal complexes: D:H.197 CLA.57: 24 residues within 4Å: Chain D: L.35, L.36, P.39, C.40, M.43, L.89, L.90, F.91, L.92, W.93, W.104, P.112, F.113, L.116, H.117, F.120 Chain G: V.40, L.43 Chain M: L.12, V.13, A.16, I.18 Ligands: CLA.17, SQD.72 21 PLIP interactions: 14 interactions with chain D, 5 interactions with chain M, 2 interactions with chain G, Hydrophobic interactions: D:P.39, D:F.91, D:F.91, D:L.92, D:W.93, D:W.93, D:L.116, D:F.120, M:L.12, M:L.12, M:V.13, M:A.16, M:I.18, G:V.40, G:L.43 Hydrogen bonds: D:L.92 Salt bridges: D:H.117 pi-Stacking: D:F.113, D:H.117, D:H.117 Metal complexes: D:H.117

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.4: 28 residues within 4Å: Chain A: L.41, A.44, T.45, F.48, F.119, I.123, Y.126, Q.130, A.146, Y.147, P.150, M.172, G.175, T.179, P.279, I.283 Chain D: L.205, A.208, L.209, A.212, I.213, W.253, F.257 Ligands: CLA.2, SQD.9, CLA.53, PL9.59, LHG.61 18 PLIP interactions: 3 interactions with chain D, 15 interactions with chain A Hydrophobic interactions: D:L.205, D:A.212, D:F.257, A:L.41, A:A.44, A:F.48, A:F.48, A:F.119, A:F.119, A:Y.126, A:A.146, A:Y.147, A:Y.147, A:P.150, A:P.279, A:I.283 Hydrogen bonds: A:Q.130, A:Y.147 PHO.54: 29 residues within 4Å: Chain A: S.209, L.210, M.214, L.258, I.259 Chain D: L.37, A.41, L.45, W.48, V.114, G.118, G.121, L.122, F.125, Q.129, N.142, A.145, F.146, P.149, F.153, F.173, G.174, V.175, I.204, P.275, V.276, L.279 Ligands: CLA.3, CLA.56 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.41, D:W.48, D:W.48, D:V.114, D:L.122, D:L.122, D:A.145, D:F.146, D:P.149, D:F.153, D:V.175, D:I.204, D:P.275, D:V.276, D:L.279, A:L.210 Hydrogen bonds: D:N.142 pi-Stacking: D:F.146

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

BCR.6: 21 residues within 4Å: Chain A: W.20, G.34, T.35, I.38, P.39, L.42, T.43, T.46, C.47, I.50, A.51, A.54, A.55, I.96, L.102, W.105, L.106, P.111 Chain H: F.15, L.18 Ligands: CLA.5 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:W.20, A:T.35, A:I.38, A:L.42, A:T.43, A:T.46, A:I.50, A:A.51, A:I.96, A:L.102, A:W.105, A:L.106, A:L.106, A:P.111, H:F.15, H:L.18 BCR.26: 13 residues within 4Å: Chain B: M.25, L.29, F.108, A.111, V.112, W.115 Chain K: I.9, A.10 Ligands: CLA.16, CLA.22, CLA.23, BCR.27, LMG.30 7 PLIP interactions: 2 interactions with chain K, 5 interactions with chain B Hydrophobic interactions: K:I.9, K:A.10, B:M.25, B:L.29, B:F.108, B:V.112, B:W.115 BCR.27: 13 residues within 4Å: Chain B: L.29, G.32, W.33, S.36, I.101, V.102, G.105 Ligands: CLA.13, CLA.16, CLA.20, CLA.22, BCR.26, LMG.30 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.33, B:I.101 BCR.28: 14 residues within 4Å: Chain B: L.103, L.106, L.107, L.109, A.110, V.112, W.113, V.116, F.117 Ligands: CLA.14, CLA.15, CLA.24, CLA.25, LMT.31 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.103, B:L.106, B:L.107, B:L.109, B:L.109, B:V.112, B:W.113, B:V.116, B:F.117 BCR.47: 11 residues within 4Å: Chain C: F.99, V.100, V.103, I.107, S.108, V.111, F.134 Chain I: Y.14 Ligands: CLA.46, SQD.50, BCR.51 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.99, C:V.100, C:V.103, C:I.107, C:V.111, C:F.134, C:F.134 BCR.48: 14 residues within 4Å: Chain C: I.196, F.197, L.200, V.214, D.219, G.223, H.224, I.227, L.251 Chain H: L.24 Ligands: CLA.34, CLA.38, CLA.39, CLA.40 8 PLIP interactions: 1 interactions with chain H, 7 interactions with chain C Hydrophobic interactions: H:L.24, C:I.196, C:F.197, C:L.200, C:V.214, C:I.227, C:I.227, C:L.251 BCR.51: 15 residues within 4Å: Chain C: A.42, G.45, L.46, L.56, F.99, L.106, S.109, A.110, G.113, A.120, L.121 Chain I: Y.14, F.17 Ligands: CLA.44, BCR.47 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain I Hydrophobic interactions: C:A.42, C:L.46, C:L.56, C:F.99, C:L.106, C:A.110, C:A.120, C:L.121, I:Y.14, I:F.17 BCR.58: 13 residues within 4Å: Chain D: F.42, M.43, G.46, G.47, L.49, T.50, W.104, L.110, F.113 Chain F: P.28, F.32, V.33 Ligands: LMG.63 11 PLIP interactions: 5 interactions with chain F, 6 interactions with chain D Hydrophobic interactions: F:P.28, F:F.32, F:F.32, F:F.32, F:V.33, D:F.42, D:L.49, D:L.49, D:W.104, D:L.110, D:F.113 BCR.73: 14 residues within 4Å: Chain G: M.31, F.34, M.35, L.37, F.38, V.40, I.44, L.55 Chain M: L.5, L.9 Ligands: CLA.10, CLA.11, CLA.12, CLA.18 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain M Hydrophobic interactions: G:F.34, G:L.37, G:F.38, G:F.38, G:F.38, G:V.40, G:I.44, G:L.55, M:L.5, M:L.9

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

SQD.7: 18 residues within 4Å: Chain A: L.200, G.204, F.265, S.270, F.273, F.274, A.277, W.278, I.281, G.282 Chain C: A.21, W.22, W.23 Chain D: N.230, F.232, R.233 Chain I: F.36 Ligands: LHG.62 18 PLIP interactions: 12 interactions with chain A, 1 interactions with chain I, 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:F.265, A:F.265, A:F.273, A:F.274, A:F.274, A:A.277, A:W.278, A:W.278, A:I.281, A:I.281, I:F.36, C:W.22, C:W.23, C:W.23 Hydrogen bonds: A:S.270, A:S.270, D:N.230 Salt bridges: D:R.233 SQD.9: 13 residues within 4Å: Chain A: W.20, N.26, R.27, I.28, V.30, I.38, L.42, T.45 Chain L: L.14 Ligands: PHO.4, CLA.53, LHG.61, SQD.71 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: A:V.30, A:L.42, L:L.14 Hydrogen bonds: A:N.26 SQD.29: 12 residues within 4Å: Chain B: R.224, L.225, K.227, A.228, R.230 Chain D: F.15 Chain G: W.25, T.28, M.31, M.35 Ligands: CLA.17, CLA.18 10 PLIP interactions: 2 interactions with chain G, 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: G:W.25, G:T.28, B:L.225, B:A.228, D:F.15 Hydrogen bonds: B:K.227 Salt bridges: B:R.224, B:R.224, B:K.227, B:R.230 SQD.50: 18 residues within 4Å: Chain C: V.48, W.84, P.97, V.101, L.104, H.105, S.108, L.112, L.161, F.164, F.168, F.169, G.170 Ligands: CLA.35, CLA.36, CLA.45, CLA.46, BCR.47 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.48, C:W.84, C:L.104, C:L.104, C:L.112, C:L.161, C:F.164, C:F.169 Hydrogen bonds: C:F.169 Salt bridges: C:K.165 SQD.69: 12 residues within 4Å: Chain J: R.16, L.19, Y.20, L.23 Chain K: F.26 Chain L: L.8, T.11, M.12, A.15, V.16, F.19, F.23 12 PLIP interactions: 4 interactions with chain J, 7 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: J:Y.20, L:L.8, L:M.12, L:A.15, L:V.16, L:F.19, L:F.19, L:F.19, K:F.26 Hydrogen bonds: J:R.16, J:R.16 Salt bridges: J:R.16 SQD.71: 8 residues within 4Å: Chain A: R.27, I.28 Chain L: L.14, F.18, I.21, A.22, F.23 Ligands: SQD.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: A:R.27, A:I.28, L:A.22 SQD.72: 10 residues within 4Å: Chain D: L.92, W.93, Q.98, G.99 Chain M: N.7, W.10, L.14, G.15, I.18 Ligands: CLA.57 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain M Hydrophobic interactions: D:W.93, D:W.93 Hydrogen bonds: M:N.7

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)

PL9.8: 11 residues within 4Å: Chain A: F.211, M.214, H.215, L.218, V.219, H.252, S.264, F.265, L.271, F.274, L.275 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.218, A:V.219, A:L.271, A:L.271, A:L.271, A:F.274, A:L.275 Hydrogen bonds: A:H.215, A:F.265 PL9.59: 32 residues within 4Å: Chain A: F.48, I.49, F.52, I.176 Chain D: M.198, M.199, A.202, G.203, L.210, H.214, T.217, Y.244, M.246, A.249, N.250, W.253, F.257, A.260, F.261, L.267, F.270, V.274 Chain J: L.25, V.28, I.31, L.32 Chain L: L.10 Ligands: PHO.4, CLA.16, CLA.53, LHG.61, LHG.67 25 PLIP interactions: 17 interactions with chain D, 3 interactions with chain J, 1 interactions with chain L, 4 interactions with chain A Hydrophobic interactions: D:M.198, D:M.199, D:A.202, D:L.210, D:T.217, D:Y.244, D:A.249, D:W.253, D:F.257, D:F.257, D:F.261, D:F.261, D:L.267, D:F.270, D:F.270, J:L.25, J:I.31, J:L.32, L:L.10, A:F.48, A:I.49, A:F.52, A:I.176 Hydrogen bonds: D:T.217, D:F.261

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

LMG.30: 16 residues within 4Å: Chain B: T.327, G.328, A.329, S.332, G.454, V.457 Chain J: F.37 Chain K: N.4, L.6, A.10, F.14, V.17 Ligands: CLA.16, BCR.26, BCR.27, LHG.67 13 PLIP interactions: 8 interactions with chain B, 2 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: B:V.457, K:V.17, J:F.37, J:F.37, J:F.37 Hydrogen bonds: B:T.327, B:T.327, B:A.329, B:S.332, B:S.332, K:N.4 Water bridges: B:T.327, B:T.327 LMG.33: 24 residues within 4Å: Chain A: F.93, W.97, E.98, F.117, L.120, I.121, F.124, L.159 Chain C: L.201, K.202, A.203, P.204, F.205, E.208, W.210, L.268, F.271, I.272 Chain H: K.5, Y.9 Ligands: CLA.5, CLA.38, CLA.39, DGD.49 21 PLIP interactions: 9 interactions with chain C, 4 interactions with chain H, 8 interactions with chain A Hydrophobic interactions: C:F.205, C:F.205, C:W.210, C:W.210, C:L.268, C:F.271, C:F.271, C:I.272, A:F.93, A:L.120, A:I.121, A:F.124, A:F.124, A:F.124, A:L.159 Hydrogen bonds: C:E.208, H:K.5, H:K.5, H:Y.9, H:Y.9, A:W.97 LMG.63: 12 residues within 4Å: Chain D: L.49, Y.67, G.70, A.71, N.72, F.73 Chain F: S.29, I.36, M.39, Q.40, R.44 Ligands: BCR.58 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain D Hydrogen bonds: F:M.39, F:Q.40, F:R.44, D:F.73 Hydrophobic interactions: D:L.49, D:F.73, D:F.73, D:F.73, D:F.73

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

LMT.31: 9 residues within 4Å: Chain B: P.88, W.91, L.149, W.162 Ligands: CLA.13, CLA.14, CLA.15, BCR.28, LMT.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.88 LMT.32: 8 residues within 4Å: Chain B: L.148, G.152, F.156, V.161, W.162 Ligands: CLA.13, CLA.15, LMT.31 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.148, B:L.148, B:F.156, B:F.156, B:W.162

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

DGD.49: 27 residues within 4Å: Chain A: L.91, S.152, T.155, I.163 Chain C: P.204, F.205, G.206, G.207, G.209, W.210, I.212, S.213, V.214, N.215, F.271, V.275, F.279, N.280, N.281, T.282, D.347, F.348, R.349, F.422, L.425 Ligands: LMG.33, CLA.38 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:P.204, C:F.205, C:F.205, C:I.212, C:F.271, C:F.271, C:V.275, C:F.422, C:L.425, A:I.163 Hydrogen bonds: C:F.205, C:G.207, C:G.209, C:W.210, C:N.281, C:N.281, C:T.282, C:T.282, C:D.347, C:D.347, C:R.349, C:R.349 DGD.65: 26 residues within 4Å: Chain B: F.193, F.250, G.254, W.257, Y.258, Y.273, Q.274, K.277, T.452 Chain D: H.87, F.120, I.123, V.154, M.159, L.162, G.163, A.290, L.291 Chain G: L.46, Y.49, N.50, V.60, D.61, W.62 Ligands: CLA.11, CLA.17 19 PLIP interactions: 7 interactions with chain G, 5 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: G:L.46, G:Y.49, G:Y.49, B:Y.258, B:T.452, D:F.120, D:I.123, D:V.154, D:L.162, D:A.290, D:L.291 Hydrogen bonds: G:N.50, G:V.60, G:D.61, G:W.62, B:K.277, B:K.277, D:H.87 Salt bridges: B:K.277

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

CL.52: 4 residues within 4Å: Chain A: N.181, H.332 Chain D: K.317, L.321 Ligand excluded by PLIP

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

BCT.55: 6 residues within 4Å: Chain A: H.215, H.272 Chain D: E.242, Y.244, H.268 Ligands: FE2.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.272

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

LHG.60: 21 residues within 4Å: Chain B: W.5, Y.6, R.7, F.464, W.468 Chain D: Y.141, I.144, R.265, W.266, F.269, F.273, T.277, W.280, M.281 Chain J: L.29 Chain K: F.14, P.18 Ligands: CLA.16, CLA.20, CLA.22, LHG.67 12 PLIP interactions: 2 interactions with chain K, 4 interactions with chain D, 5 interactions with chain B, 1 interactions with chain J Hydrophobic interactions: K:F.14, K:P.18, D:F.273, D:W.280, B:W.5, B:F.464, J:L.29 Hydrogen bonds: D:Y.141, D:Y.141 Water bridges: B:R.7, B:R.7 Salt bridges: B:R.7 LHG.61: 29 residues within 4Å: Chain A: I.28, M.37, R.129 Chain D: I.256, F.257, I.259, A.260, F.261, S.262, N.263, W.266, F.270 Chain J: N.15, T.17, S.18, Y.20, L.21, L.24 Chain L: A.13, L.14, L.17, A.20, I.21 Ligands: CLA.2, PHO.4, SQD.9, CLA.53, PL9.59, LHG.67 17 PLIP interactions: 6 interactions with chain L, 1 interactions with chain A, 4 interactions with chain J, 6 interactions with chain D Hydrophobic interactions: L:L.14, L:L.17, L:A.20, L:I.21, A:I.28, J:Y.20, J:L.21, J:L.24, D:F.257, D:I.259, D:F.261, D:F.270 Hydrogen bonds: L:E.25, L:E.25, J:N.15, D:S.262, D:N.263 LHG.62: 23 residues within 4Å: Chain A: R.140, W.142, A.146, F.273, A.277, V.280, I.281, W.284, F.285 Chain C: F.20, W.23, W.430, R.434 Chain D: A.216, E.219, N.220, S.229, N.230, T.231, F.232 Ligands: SQD.7, CLA.37, CLA.41 17 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: A:A.146, A:F.273, A:V.280, A:I.281, A:I.281, A:W.284, A:F.285, C:W.23, C:W.23, C:W.430, D:A.216, D:E.219 Salt bridges: A:R.140 Hydrogen bonds: C:R.434, D:S.229, D:S.229, D:T.231 LHG.67: 24 residues within 4Å: Chain B: P.4, W.5, Y.6 Chain D: A.202, R.265, W.266, F.269, F.273 Chain J: E.13, L.14, N.15, S.18, L.21, G.22, L.25, V.28 Chain K: F.21 Ligands: CLA.20, CLA.22, LMG.30, CLA.53, PL9.59, LHG.60, LHG.61 14 PLIP interactions: 1 interactions with chain K, 2 interactions with chain B, 6 interactions with chain J, 5 interactions with chain D Hydrophobic interactions: K:F.21, J:L.21, J:L.25, J:V.28, D:A.202, D:F.269, D:F.273, D:F.273 Hydrogen bonds: B:W.5, B:Y.6, J:E.13, J:N.15, J:S.18 Salt bridges: D:R.265

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

HEM.64: 16 residues within 4Å: Chain E: P.9, I.13, R.18, Y.19, H.23, T.26, I.27, L.30 Chain F: I.14, R.18, W.19, V.22, H.23, A.26, V.27, V.30 16 PLIP interactions: 7 interactions with chain E, 9 interactions with chain F, Hydrophobic interactions: E:I.13, E:Y.19, E:T.26, E:I.27, E:I.27, F:I.14, F:V.22, F:A.26, F:V.27, F:V.30 Salt bridges: E:R.18, F:R.18 pi-Stacking: E:Y.19, F:W.19, F:H.23 Metal complexes: F:H.23

3 x FME: N-FORMYLMETHIONINE(Non-covalent)

FME.66: 7 residues within 4Å: Chain A: I.96, W.97, A.99 Chain H: L.2, T.3, L.4, K.5 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:T.3, H:L.4, H:K.5 Hydrophobic interactions: A:W.97 FME.68: 7 residues within 4Å: Chain A: G.74 Chain D: S.300, Q.301, R.304 Chain K: Q.2, V.3 Chain L: E.2 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:V.3, L:E.2 FME.70: 4 residues within 4Å: Chain K: F.8 Chain L: E.2, S.3, V.4 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:E.2, L:E.2, L:S.3, L:V.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gisriel, C.J. et al., Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex. Joule (2020)

Release Date

2020-08-26

Peptides

Photosystem II protein D1 2: A
Photosystem II CP47 reaction center protein: B
Photosystem II CP43 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 K: I
Photosystem II reaction center protein L: J
Photosystem II reaction center protein M: K
Photosystem II reaction center protein T: L
Photosystem II reaction center X protein: M

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
K

J
L

K
M

L
T

M
X

Membrane

We predict this structure to be a membrane protein.
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Photosystem II protein D1 2

Photosystem II CP47 reaction center protein

Photosystem II CP43 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 K

Photosystem II reaction center protein L

Photosystem II reaction center protein M

Photosystem II reaction center protein T

Photosystem II reaction center X protein

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