SMTL ID : 7nho.1

Structure of PSII-M

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: H.215, H.272 Chain D: H.214, H.268 Ligands: BCT.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Metal complexes: A:H.215, A:H.272, D:H.214

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: D.170, E.189, L.343 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.170

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

CL.3: 4 residues within 4Å: Chain A: N.181, V.185, H.332, R.334 Ligand excluded by PLIP

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.4: 20 residues within 4Å: Chain A: L.41, A.44, T.45, F.48, F.119, Y.126, Q.130, Y.147, P.150, G.175, I.176, V.283 Chain D: A.208, L.209, I.213, W.253, F.257 Ligands: CLA.5, CLA.6, LMG.51 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.41, A:A.44, A:F.48, A:F.119, A:F.119, A:Y.147, A:I.176, A:V.283, D:L.209 Hydrogen bonds: A:Q.130 PHO.53: 22 residues within 4Å: Chain A: F.206, L.210, M.214, L.258 Chain D: L.37, A.41, A.44, L.45, W.48, G.118, F.125, Q.129, N.142, F.146, P.149, F.173, G.174, V.175, V.276, L.279 Ligands: CLA.7, CLA.54 18 PLIP interactions: 2 interactions with chain A, 16 interactions with chain D Hydrophobic interactions: A:F.206, A:L.210, D:L.37, D:A.44, D:L.45, D:W.48, D:W.48, D:F.125, D:F.146, D:F.146, D:P.149, D:F.173, D:F.173, D:V.175, D:V.276, D:L.279 Hydrogen bonds: D:Q.129, D:N.142

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.5: 19 residues within 4Å: Chain A: Y.147, P.150, S.153, M.183, F.186, I.192, L.193, H.198, G.201, V.205, T.286, A.287, I.290 Chain D: L.182 Ligands: PHO.4, CLA.6, CLA.7, LMG.51, CLA.54 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D, Hydrophobic interactions: A:M.183, A:F.186, A:I.192, A:L.193, A:V.205, D:L.182, D:L.182 Metal complexes: A:H.198 CLA.6: 16 residues within 4Å: Chain A: F.48, F.158, M.172, I.176, T.179, F.180, M.183 Chain D: M.198, V.201, A.202 Ligands: PHO.4, CLA.5, LMG.13, LMG.51, PL9.52, CLA.54 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A, Hydrophobic interactions: D:V.201, D:A.202, A:F.48, A:F.158, A:I.176 CLA.7: 15 residues within 4Å: Chain A: Q.199, V.202, A.203, L.210, I.259, W.278 Chain D: F.157, V.175, I.178, F.179, L.182 Ligands: CLA.5, LMG.50, PHO.53, CLA.54 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A, Hydrophobic interactions: D:F.157, D:I.178, D:F.179, D:L.182, A:L.210, A:I.259, A:W.278 CLA.8: 17 residues within 4Å: Chain A: I.36, P.39, T.40, F.93, P.95, I.96, L.114, F.117, H.118, L.121 Chain H: V.8, Y.9, V.12, T.13, F.15 Ligands: BCR.9, CLA.38 9 PLIP interactions: 3 interactions with chain H, 6 interactions with chain A, Hydrophobic interactions: H:Y.9, H:F.15, H:F.15, A:T.40, A:F.93, A:I.96, A:L.121 Hydrogen bonds: A:I.96 Salt bridges: A:H.118 CLA.14: 7 residues within 4Å: Chain B: W.185, G.186, A.204, I.207 Chain G: F.41 Ligands: CLA.15, BCR.58 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain G, Hydrophobic interactions: B:W.185, B:A.204, B:I.207, G:F.41, G:F.41 CLA.15: 22 residues within 4Å: Chain B: G.189, F.190, P.192, G.197, A.200, H.201, A.204, A.205, V.208, F.250, V.251 Chain D: L.158, I.159, L.162 Chain G: F.41, L.42, I.45, L.46 Ligands: CLA.14, CLA.16, CLA.22, BCR.58 15 PLIP interactions: 9 interactions with chain B, 3 interactions with chain D, 3 interactions with chain G, Hydrophobic interactions: B:F.190, B:F.190, B:A.200, B:H.201, B:A.204, B:V.208, B:F.250, D:L.158, D:I.159, D:L.162, G:F.41, G:L.42, G:I.45 pi-Stacking: B:F.190 Metal complexes: B:H.201 CLA.16: 22 residues within 4Å: Chain B: R.68, L.69, L.149, C.150, F.153, L.158, M.166, V.198, H.201, H.202, F.247, A.248, V.251, V.252, T.262 Ligands: CLA.15, CLA.17, CLA.18, CLA.19, CLA.21, CLA.22, CLA.23 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.149, B:F.153, B:V.198, B:F.247, B:V.251, B:V.252 Salt bridges: B:R.68 pi-Cation interactions: B:H.201 Metal complexes: B:H.202 CLA.17: 23 residues within 4Å: Chain B: W.33, F.61, F.65, R.68, L.145, L.148, L.149, V.245, A.248, A.249, V.252, F.451, H.455, F.458, F.462 Ligands: CLA.16, CLA.18, CLA.20, CLA.23, CLA.24, CLA.25, CLA.26, CLA.28 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.33, B:F.61, B:F.65, B:L.145, B:L.148, B:V.245, B:A.248, B:A.249, B:F.458, B:F.458, B:F.462, B:F.462 Salt bridges: B:R.68 pi-Stacking: B:H.455 CLA.18: 21 residues within 4Å: Chain B: T.27, V.30, A.31, A.34, V.62, F.65, M.66, R.68, L.69, V.96, H.100, L.103, G.147, C.150, A.205, G.209 Ligands: CLA.16, CLA.17, CLA.19, CLA.25, CLA.28 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:T.27, B:A.31, B:A.34, B:L.69, B:V.96 Salt bridges: B:R.68 Metal complexes: B:H.100 CLA.19: 21 residues within 4Å: Chain B: L.69, V.71, W.91, V.96, A.99, H.100, V.102, L.103, L.106, L.149, G.152, F.153, F.156, H.157, F.162, G.163, P.164 Ligands: CLA.16, CLA.18, CLA.29, BCR.32 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.69, B:V.71, B:W.91, B:W.91, B:V.96, B:V.102, B:L.103, B:L.106, B:L.106, B:L.149, B:F.153, B:F.156 Metal complexes: B:H.157 CLA.20: 16 residues within 4Å: Chain B: W.33, M.37, Y.40, Q.58, G.59, F.61, T.327, G.328, P.329, W.450, A.454 Chain D: M.281 Ligands: CLA.17, CLA.26, BCR.31, LMG.49 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:W.33, B:Y.40, B:F.61, B:F.61, B:W.450, B:W.450, B:A.454 Hydrogen bonds: B:Y.40, B:E.41, B:G.328 pi-Stacking: B:F.61 CLA.21: 17 residues within 4Å: Chain B: T.236, S.239, S.240, A.243, F.247, F.463, H.466, T.473 Chain D: F.120, I.123, M.126, L.127 Chain G: L.39 Ligands: CLA.16, CLA.22, CLA.23, CLA.55 11 PLIP interactions: 4 interactions with chain D, 6 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: D:F.120, D:I.123, D:L.127, D:L.127, B:A.243, B:F.247, B:F.463, G:L.39 Hydrogen bonds: B:S.239 Salt bridges: B:H.466 pi-Stacking: B:H.466 CLA.22: 19 residues within 4Å: Chain B: F.139, V.208, A.212, F.215, H.216, V.219, P.221, P.222, L.225, L.229 Chain G: T.27, M.31, F.34, L.39 Ligands: CLA.15, CLA.16, CLA.21, CLA.23, BCR.58 7 PLIP interactions: 2 interactions with chain G, 5 interactions with chain B, Hydrophobic interactions: G:F.34, G:L.39, B:F.139, B:V.208, B:A.212, B:F.215 Salt bridges: B:H.216 CLA.23: 16 residues within 4Å: Chain B: L.135, M.138, F.139, H.142, L.143, L.145, A.146, M.231, V.237, S.240, S.241 Ligands: CLA.16, CLA.17, CLA.21, CLA.22, CLA.25 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:F.139, B:L.145, B:A.146, B:V.237, B:V.237 Hydrogen bonds: B:H.142 CLA.24: 19 residues within 4Å: Chain B: W.5, Y.6, R.7, V.8, H.9, T.10, L.238, L.461, F.462, G.465, W.468, H.469, R.472 Ligands: LMG.13, CLA.17, CLA.25, CLA.26, CLA.27, LMG.49 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:W.5, B:V.8, B:H.9, B:T.10, B:L.238, B:F.462, B:F.462 Salt bridges: B:H.9, B:R.472 Metal complexes: B:H.469 CLA.25: 19 residues within 4Å: Chain B: H.9, L.12, I.13, L.19, A.22, H.23, H.26, T.27, V.237, L.238, S.241, V.245 Ligands: CLA.17, CLA.18, CLA.23, CLA.24, CLA.26, CLA.27, CLA.28 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:L.12, B:I.13, B:H.23, B:H.26, B:T.27, B:V.237, B:L.238 Hydrogen bonds: B:S.241 Salt bridges: B:H.23 pi-Stacking: B:H.26 Metal complexes: B:H.23 CLA.26: 16 residues within 4Å: Chain B: H.9, H.26, V.30, W.33, F.458, L.461, F.462 Ligands: LMG.13, CLA.17, CLA.20, CLA.24, CLA.25, CLA.27, BCR.30, BCR.31, LMG.49 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:V.30, B:V.30, B:W.33, B:L.461, B:F.462, B:F.462 Salt bridges: B:H.9 pi-Stacking: B:H.26 CLA.27: 15 residues within 4Å: Chain B: V.8, H.9, V.11, L.12, A.22, L.29, W.115 Chain J: Q.8, V.10 Chain K: F.21 Ligands: LMG.13, CLA.24, CLA.25, CLA.26, BCR.30 9 PLIP interactions: 2 interactions with chain K, 7 interactions with chain B, Hydrophobic interactions: K:F.21, K:F.21, B:V.8, B:L.12, B:L.29, B:W.115, B:W.115 pi-Stacking: B:H.9 Metal complexes: B:H.9 CLA.28: 15 residues within 4Å: Chain B: I.20, H.23, L.24, L.133, M.138, I.141, H.142, L.145 Chain G: L.14, N.15 Ligands: CLA.17, CLA.18, CLA.25, CLA.29, BCR.32 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain B, Hydrophobic interactions: G:L.14, B:L.133, B:L.133, B:I.141 CLA.29: 11 residues within 4Å: Chain B: L.24, A.110, W.113, H.114, L.120 Chain G: T.5, L.7, G.8 Ligands: CLA.19, CLA.28, BCR.32 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: B:L.24, B:A.110, B:W.113, B:W.113, B:L.120, G:L.7 pi-Stacking: B:W.113, B:W.113 Metal complexes: B:H.114 CLA.34: 20 residues within 4Å: Chain C: L.156, G.159, A.160, L.163, W.211, V.221, H.225, I.228, A.266, M.269, M.270, I.273, F.277, V.284, Y.285 Ligands: CLA.35, CLA.36, CLA.39, CLA.40, BCR.46 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.163, C:W.211, C:I.228, C:A.266, C:M.270, C:I.273, C:V.284, C:Y.285 Hydrogen bonds: C:Y.285 Salt bridges: C:H.225 Metal complexes: C:H.225 CLA.35: 19 residues within 4Å: Chain C: L.76, H.79, L.162, A.165, F.170, L.267, M.270, A.274, V.278, Y.285, H.418, L.421, A.422, F.425 Ligands: CLA.34, CLA.36, CLA.37, CLA.44, CLA.47 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:L.76, C:A.165, C:F.170, C:A.274, C:F.425 Salt bridges: C:H.79, C:H.418 pi-Cation interactions: C:H.418 CLA.36: 17 residues within 4Å: Chain C: I.48, V.49, W.51, A.52, T.56, L.76, H.79, L.83, V.102, H.106, L.267, M.270 Ligands: LMG.33, CLA.34, CLA.35, CLA.44, CLA.47 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:I.48, C:V.49, C:A.52, C:H.79, C:L.83, C:V.102, C:L.267 Salt bridges: C:H.79 CLA.37: 12 residues within 4Å: Chain C: W.51, F.58, G.73, I.75, L.392, S.394, W.413, S.417 Chain I: P.26 Ligands: CLA.35, CLA.41, CLA.47 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:W.51, C:F.58, C:F.58, C:I.75, C:L.392, C:W.413, C:W.413 Hydrogen bonds: C:S.394 CLA.38: 18 residues within 4Å: Chain A: F.33, M.127, W.131 Chain C: F.252, S.261, Y.262, G.265, A.266, H.429, A.433, R.437 Chain H: V.12, V.16, F.19, F.23 Ligands: CLA.8, CLA.40, BCR.46 11 PLIP interactions: 5 interactions with chain C, 4 interactions with chain H, 2 interactions with chain A, Hydrophobic interactions: C:Y.262, H:V.12, H:V.16, H:F.19, H:F.23, A:F.33, A:W.131 Hydrogen bonds: C:S.261, C:Y.262 Salt bridges: C:R.437 Metal complexes: C:H.429 CLA.39: 18 residues within 4Å: Chain C: L.149, L.153, L.201, I.231, C.232, G.235, W.238, H.239, T.242, P.244, F.245, W.247, A.248, A.251, F.252 Ligands: CLA.34, CLA.40, BCR.46 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.149, C:L.153, C:A.248, C:F.252 Hydrogen bonds: C:F.245 CLA.40: 17 residues within 4Å: Chain C: M.145, T.146, L.149, H.152, L.156, C.232, F.252, W.254, Y.259, Y.262, S.263, M.270 Ligands: CLA.34, CLA.38, CLA.39, CLA.42, BCR.46 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:M.145, C:T.146, C:L.149, C:F.252, C:W.254, C:Y.259, C:Y.259, C:Y.262, C:Y.262, C:Y.262, C:Y.262 CLA.41: 21 residues within 4Å: Chain C: W.24, A.25, G.26, N.27, A.28, E.257, L.260, L.264, F.424, F.425, G.428, W.431, H.432, R.435 Chain I: V.30, F.37 Ligands: LHG.10, CLA.37, CLA.42, CLA.43, CLA.47 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain I, Hydrophobic interactions: C:A.28, C:L.260, C:L.264, C:F.425, C:F.425, C:W.431, I:V.30 Hydrogen bonds: C:N.27 Salt bridges: C:H.432, C:R.435 Metal complexes: C:H.432 CLA.42: 21 residues within 4Å: Chain C: N.27, L.30, L.37, A.40, H.41, H.44, Y.137, W.139, M.145, H.152, L.156, G.256, Y.259, L.260, S.263, L.264, L.267 Ligands: CLA.40, CLA.41, CLA.44, CLA.47 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:N.27, C:L.30, C:L.37, C:A.40, C:H.44, C:Y.137, C:Y.137, C:W.139, C:W.139, C:L.156, C:Y.259, C:L.260 Hydrogen bonds: C:S.263 pi-Cation interactions: C:H.41 Metal complexes: C:H.41 CLA.43: 28 residues within 4Å: Chain C: R.14, D.15, W.23, G.26, N.27, R.29, L.30, K.36, A.40, L.47, A.111, G.114, F.115, I.122 Chain I: F.32, L.33, A.36, F.37, W.39, Q.40 Chain N: I.35, N.45, L.46 Chain O: V.20, V.23 Ligands: CLA.41, CLA.47, BCR.62 12 PLIP interactions: 5 interactions with chain I, 5 interactions with chain C, 1 interactions with chain N, 1 interactions with chain O, Hydrophobic interactions: I:F.32, I:L.33, I:F.37, I:W.39, C:L.30, C:L.47, C:I.122, N:I.35, O:V.23 pi-Stacking: I:W.39 Hydrogen bonds: C:R.29 Salt bridges: C:K.36 CLA.44: 17 residues within 4Å: Chain C: L.38, H.41, V.42, A.45, L.113, F.134, F.135, Y.137, F.151, H.152, V.155, L.156 Ligands: CLA.35, CLA.36, CLA.42, CLA.45, BCR.48 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.38, C:L.113, C:F.134, C:F.135, C:Y.137, C:V.155 CLA.45: 10 residues within 4Å: Chain C: L.38, V.42, V.112, G.116, Y.119, H.120, Y.131, F.135 Ligands: CLA.44, BCR.48 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:L.38, C:Y.119, C:Y.119, C:Y.131, C:F.135, C:F.135 pi-Stacking: C:H.120, C:H.120 Metal complexes: C:H.120 CLA.47: 16 residues within 4Å: Chain C: N.27, H.44, L.47, W.51, L.267, F.424, F.425 Chain I: P.29, V.30, L.33 Ligands: CLA.35, CLA.36, CLA.37, CLA.41, CLA.42, CLA.43 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain I, Hydrophobic interactions: C:L.47, C:W.51, C:L.267, C:F.424, C:F.425, I:P.29, I:V.30, I:L.33 Hydrogen bonds: C:N.27 pi-Cation interactions: C:H.44 CLA.54: 28 residues within 4Å: Chain A: M.183, F.206 Chain D: L.45, W.48, F.146, P.149, V.152, S.155, V.156, F.181, L.182, F.185, Q.186, W.191, T.192, H.197, G.200, V.201, V.204, L.205, L.279, S.282, A.283 Ligands: CLA.5, CLA.6, CLA.7, LMG.50, PHO.53 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:L.45, D:W.48, D:F.146, D:P.149, D:F.181, D:F.185, D:Q.186, D:W.191, D:T.192, D:V.204, D:V.204, D:L.205, D:L.279 pi-Stacking: D:W.191 pi-Cation interactions: D:H.197 Metal complexes: D:H.197 CLA.55: 20 residues within 4Å: Chain D: C.40, L.43, L.89, L.90, L.91, W.93, W.104, T.112, F.113, L.116, H.117, F.120 Chain G: L.37, V.40, L.43 Chain M: G.13, L.14, L.21 Ligands: CLA.21, BCR.58 14 PLIP interactions: 2 interactions with chain M, 9 interactions with chain D, 3 interactions with chain G, Hydrophobic interactions: M:L.14, M:L.21, D:L.43, D:L.91, D:W.93, D:W.93, D:L.116, D:F.120, G:L.37, G:V.40, G:L.43 Salt bridges: D:H.117 pi-Stacking: D:H.117 Metal complexes: D:H.117

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

BCR.9: 15 residues within 4Å: Chain A: V.35, L.42, A.43, I.46, C.47, I.50, A.51, A.54, A.55, L.102, L.106, P.111, L.114 Ligands: CLA.8, LMG.59 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.35, A:L.42, A:I.46, A:I.50, A:A.51, A:L.102, A:L.106, A:P.111, A:L.114 BCR.30: 5 residues within 4Å: Chain B: M.25, W.115 Ligands: CLA.26, CLA.27, BCR.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.115, B:W.115 BCR.31: 10 residues within 4Å: Chain B: G.32, W.33, S.36, I.101, S.104, G.105, F.108 Ligands: CLA.20, CLA.26, BCR.30 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.33, B:F.108 BCR.32: 7 residues within 4Å: Chain B: L.106, L.109, C.112, W.113 Ligands: CLA.19, CLA.28, CLA.29 No protein-ligand interaction detected (PLIP) BCR.46: 12 residues within 4Å: Chain C: I.197, L.201, V.215, D.220, V.221, I.228 Chain H: V.20, F.23 Ligands: CLA.34, CLA.38, CLA.39, CLA.40 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:I.197, C:L.201, C:L.201, C:V.215, C:I.228, C:I.228, H:F.23 BCR.48: 11 residues within 4Å: Chain C: V.104, V.105, I.108, V.112, F.135 Chain I: Y.15 Chain O: V.51, G.55 Ligands: LMG.33, CLA.44, CLA.45 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.105, C:I.108, C:I.108, C:V.112, C:F.135 BCR.57: 9 residues within 4Å: Chain D: Y.42, G.46, L.49, T.50, L.110 Chain F: P.29, T.30, F.33 Ligands: LMG.50 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:P.29, F:F.33, F:F.33, D:Y.42, D:L.49, D:T.50, D:L.110 BCR.58: 10 residues within 4Å: Chain G: F.34, M.35, L.37, F.38, F.41 Chain M: L.7 Ligands: CLA.14, CLA.15, CLA.22, CLA.55 5 PLIP interactions: 1 interactions with chain M, 4 interactions with chain G Hydrophobic interactions: M:L.7, G:F.34, G:F.38, G:F.38, G:F.41 BCR.60: 13 residues within 4Å: Chain I: I.28, L.31, A.34, L.35, F.37, V.38 Chain N: I.28, G.29, G.32 Chain O: V.13, S.16, F.17 Ligands: BCR.62 9 PLIP interactions: 6 interactions with chain I, 1 interactions with chain O, 2 interactions with chain N Hydrophobic interactions: I:I.28, I:L.31, I:A.34, I:L.35, I:F.37, I:V.38, O:V.13, N:I.28, N:I.28 BCR.62: 20 residues within 4Å: Chain C: A.43, G.46, L.47, F.50, V.104, I.108, S.110, A.111, G.114 Chain I: Y.15, L.21, F.32, L.35, A.36, W.39 Chain O: L.9, V.13, S.16 Ligands: CLA.43, BCR.60 14 PLIP interactions: 7 interactions with chain I, 5 interactions with chain C, 2 interactions with chain O Hydrophobic interactions: I:Y.15, I:Y.15, I:L.21, I:F.32, I:L.35, I:A.36, I:W.39, C:L.47, C:F.50, C:V.104, C:I.108, C:A.111, O:L.9, O:V.13

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

LHG.10: 16 residues within 4Å: Chain A: R.140, W.142, S.270, F.273, W.284 Chain C: W.24, W.431, R.435 Chain D: E.219, N.220, A.229, S.230, T.231, F.232 Ligands: LHG.11, CLA.41 8 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: C:W.24, C:W.24, A:W.284, D:E.219 Hydrogen bonds: C:W.431, D:N.220, D:T.231 Salt bridges: A:R.140 LHG.11: 7 residues within 4Å: Chain A: Y.262, A.263, S.264, F.265, N.266, S.270 Ligands: LHG.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.262, A:A.263, A:F.265 Hydrogen bonds: A:N.266, A:S.270

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

BCT.12: 9 residues within 4Å: Chain A: H.215, Y.246, H.272 Chain D: H.214, V.218, Y.244, K.264, H.268 Ligands: FE.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.246, A:H.272

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

LMG.13: 22 residues within 4Å: Chain A: N.234, Y.235 Chain B: P.4, W.5, Y.6 Chain D: W.266, F.269, F.273 Chain J: E.11, L.12, N.13, S.16, G.20, V.26 Chain K: V.17 Ligands: CLA.6, CLA.24, CLA.26, CLA.27, LMG.49, LMG.51, PL9.52 11 PLIP interactions: 1 interactions with chain D, 5 interactions with chain J, 1 interactions with chain B, 1 interactions with chain K, 3 interactions with chain A Hydrophobic interactions: D:F.269, J:V.26, B:W.5, K:V.17 Hydrogen bonds: J:E.11, J:N.13, J:N.13, J:S.16, A:N.234, A:Y.235, A:Y.235 LMG.33: 10 residues within 4Å: Chain C: W.85, F.97, V.101, V.105, H.106 Chain I: P.12 Chain O: F.59, V.62 Ligands: CLA.36, BCR.48 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain O Hydrophobic interactions: C:W.85, C:F.97, C:V.101, C:V.101, C:V.105, C:V.105, O:F.59, O:F.59 LMG.49: 17 residues within 4Å: Chain A: A.233, N.234 Chain B: Y.6, R.7 Chain D: Y.141, W.266, F.269, F.273, T.277, W.280 Chain J: I.24 Chain K: F.14, V.17 Ligands: LMG.13, CLA.20, CLA.24, CLA.26 11 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 3 interactions with chain K, 3 interactions with chain D, 1 interactions with chain J Hydrophobic interactions: B:Y.6, K:F.14, K:F.14, K:V.17, D:F.269, D:F.273, D:F.273, J:I.24 Hydrogen bonds: B:Y.6, B:R.7, A:N.234 LMG.50: 15 residues within 4Å: Chain A: P.196, Q.199, L.200 Chain D: Y.67, G.70, C.71, N.72, F.73, L.74 Chain F: I.37, M.40, Q.41 Ligands: CLA.7, CLA.54, BCR.57 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: A:P.196, A:Q.199, A:L.200, D:F.73, D:L.74 Hydrogen bonds: F:Q.41 LMG.51: 24 residues within 4Å: Chain A: I.38 Chain D: I.256, F.257, I.259, A.260, F.261, S.262, N.263, W.266, F.270 Chain J: N.13, T.15, Y.18, L.19, L.22 Chain L: F.10, I.13, F.17, A.20 Ligands: PHO.4, CLA.5, CLA.6, LMG.13, PL9.52 15 PLIP interactions: 1 interactions with chain A, 4 interactions with chain J, 4 interactions with chain L, 6 interactions with chain D Hydrophobic interactions: A:I.38, J:Y.18, J:L.19, J:L.22, L:F.10, L:I.13, L:F.17, L:A.20, D:F.257, D:I.259, D:I.259, D:I.259, D:F.261, D:F.270 Hydrogen bonds: J:N.13 LMG.59: 3 residues within 4Å: Chain H: M.1, T.3 Ligands: BCR.9 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:T.3 LMG.61: 8 residues within 4Å: Chain J: R.14, Y.18 Chain K: E.30, S.31, Q.32, Q.33, K.34 Chain L: F.19 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain J, 1 interactions with chain L Hydrogen bonds: K:K.34 Hydrophobic interactions: J:Y.18, L:F.19

1 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)

PL9.52: 27 residues within 4Å: Chain A: F.48, F.52, I.176 Chain D: M.199, A.202, G.203, L.209, H.214, T.217, M.246, A.249, N.250, W.253, I.259, A.260, F.261, L.267, F.273, V.274, T.277 Chain J: V.26, L.29, L.30 Chain L: F.10 Ligands: CLA.6, LMG.13, LMG.51 22 PLIP interactions: 4 interactions with chain J, 14 interactions with chain D, 3 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: J:V.26, J:L.29, J:L.30, J:L.30, D:M.199, D:A.202, D:A.249, D:W.253, D:I.259, D:F.261, D:L.267, D:F.273, D:V.274, D:V.274, D:T.277, A:F.48, A:F.52, A:I.176, L:F.10 Hydrogen bonds: D:H.214, D:T.217, D:F.261

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

HEM.56: 12 residues within 4Å: Chain E: R.8, I.13, R.18, I.22, H.23, I.27 Chain F: Y.13, R.19, W.20, H.24, A.27, I.31 13 PLIP interactions: 7 interactions with chain E, 6 interactions with chain F, Hydrophobic interactions: E:I.22, E:I.27, F:A.27, F:I.31 Hydrogen bonds: E:R.8, F:Y.13 Salt bridges: E:R.8, E:R.18, F:R.19 pi-Stacking: E:Y.19 Metal complexes: E:H.23, F:H.24 pi-Cation interactions: F:H.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zabret, J. et al., Structural insights into photosystem II assembly. Nat.Plants (2021)

Release Date

2021-05-05

Peptides

Photosystem II protein D1 1: 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
Photosystem II reaction center protein Ycf12: N
Photosystem II reaction center protein Z: O

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

N
y

O
Z

Membrane

We predict this structure to be a membrane protein.
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Photosystem II protein D1 1

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

Photosystem II reaction center protein Ycf12

Photosystem II reaction center protein Z

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