SMTL ID : 7nhp.1

Structure of PSII-I (PSII with Psb27, Psb28, and Psb34)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

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

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

CL.2: 2 residues within 4Å: Chain A: N.181, H.332 Ligand excluded by PLIP

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.3: 20 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, L.174, G.175, V.283 Chain D: L.205, L.209, I.213, W.253 Ligands: CLA.4, CLA.5 15 PLIP interactions: 3 interactions with chain D, 12 interactions with chain A Hydrophobic interactions: D:L.205, D:L.209, D:I.213, A:L.41, A:A.44, A:F.48, A:I.115, A:F.119, A:Y.126, A:Y.147, A:P.150, A:L.174, A:V.283 Hydrogen bonds: A:Y.126, A:Q.130 PHO.53: 20 residues within 4Å: Chain A: F.206, A.209, L.210, M.214 Chain D: A.44, W.48, G.118, L.122, F.125, Q.129, A.145, F.146, P.149, F.173, G.174, I.178, P.275, L.279 Ligands: CLA.6, CLA.54 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.44, D:W.48, D:W.48, D:L.122, D:F.125, D:A.145, D:F.173, D:I.178, D:P.275, D:L.279, A:F.206 Hydrogen bonds: D:Q.129

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.4: 25 residues within 4Å: Chain A: Y.147, P.150, S.153, V.157, F.182, M.183, F.186, Q.187, I.192, H.198, G.201, V.202, V.205, F.206, V.283, T.286, A.287, I.290 Chain D: F.257 Chain L: F.17 Ligands: PHO.3, CLA.5, CLA.6, LMG.51, CLA.54 13 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D, 1 interactions with chain L, Hydrophobic interactions: A:Y.147, A:P.150, A:F.182, A:F.186, A:Q.187, A:I.192, A:V.202, A:V.205, A:F.206, D:F.257, L:F.17 Hydrogen bonds: A:S.153 Metal complexes: A:H.198 CLA.5: 16 residues within 4Å: Chain A: T.45, F.158, M.172, I.176, T.179, F.180, M.183 Chain D: M.198, V.201, A.202 Chain L: F.10 Ligands: PHO.3, CLA.4, LMG.48, LMG.51, PL9.52 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain L, 3 interactions with chain A, Hydrophobic interactions: D:V.201, L:F.10, A:F.158, A:T.179, A:F.180 CLA.6: 12 residues within 4Å: Chain A: Q.199, V.202, A.203 Chain D: F.157, V.175, I.178, L.182 Ligands: CLA.4, LMG.50, PHO.53, CLA.54, BCR.56 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D, Hydrophobic interactions: A:V.202, D:F.157, D:V.175, D:I.178, D:L.182 CLA.7: 16 residues within 4Å: Chain A: P.39, T.40, F.93, Y.94, P.95, I.96, W.97, L.114, F.117, H.118, L.121 Chain H: V.8, Y.9, V.12, T.13, F.15 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain H, Hydrophobic interactions: A:P.39, A:T.40, A:F.93, A:L.114, A:F.117, H:Y.9, H:T.13, H:F.15 Hydrogen bonds: A:I.96 Metal complexes: A:H.118 CLA.10: 11 residues within 4Å: Chain B: W.185, P.187, F.190, A.204, I.207 Chain G: F.41 Chain R: V.49, A.52, V.53 Ligands: CLA.11, BCR.58 11 PLIP interactions: 2 interactions with chain G, 2 interactions with chain R, 7 interactions with chain B, Hydrophobic interactions: G:F.41, G:F.41, R:V.49, R:A.52, B:W.185, B:W.185, B:W.185, B:W.185, B:F.190, B:A.204, B:I.207 CLA.11: 23 residues within 4Å: Chain B: G.189, F.190, P.192, G.197, V.198, A.200, H.201, A.204, V.208, F.247, F.250, V.251 Chain D: I.159, L.162 Chain G: F.38, F.41, L.42, I.45, L.46, Y.49 Ligands: CLA.10, CLA.12, BCR.58 19 PLIP interactions: 12 interactions with chain B, 5 interactions with chain G, 2 interactions with chain D, Hydrophobic interactions: B:F.190, B:F.190, B:P.192, B:A.200, B:H.201, B:V.208, B:V.208, B:F.247, B:F.250, B:F.250, B:F.250, G:F.38, G:F.41, G:L.42, G:I.45, D:I.159, D:L.162 Metal complexes: B:H.201 pi-Stacking: G:F.41 CLA.12: 21 residues within 4Å: Chain B: R.68, L.69, A.146, L.149, C.150, F.153, V.198, H.201, H.202, F.247, A.248, V.251, V.252, T.262 Chain G: M.35 Ligands: CLA.11, CLA.13, CLA.14, CLA.15, CLA.18, BCR.58 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.149, B:F.153, B:F.247, B:F.247, B:A.248, B:V.251, B:V.252 Hydrogen bonds: B:R.68 Salt bridges: B:R.68 CLA.13: 20 residues within 4Å: Chain B: W.33, F.65, R.68, L.149, V.245, A.248, A.249, F.451, H.455, F.458, F.462 Ligands: CLA.12, CLA.14, CLA.16, CLA.19, CLA.20, CLA.21, CLA.22, CLA.24, BCR.27 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:W.33, B:F.65, B:L.149, B:V.245, B:A.248, B:A.249, B:F.451, B:F.458, B:F.458, B:F.462, B:F.462 Salt bridges: B:R.68 Metal complexes: B:H.455 CLA.14: 21 residues within 4Å: Chain B: T.27, V.30, A.31, W.33, A.34, V.62, F.65, M.66, R.68, L.69, H.100, L.103, A.146, G.147 Ligands: CLA.12, CLA.13, CLA.15, CLA.18, CLA.19, CLA.21, CLA.24 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:T.27, B:V.30, B:W.33, B:A.34, B:L.69, B:L.103 CLA.15: 18 residues within 4Å: Chain B: L.69, G.70, V.71, W.91, V.96, A.99, V.102, L.106, G.152, F.153, F.156, H.157, F.162, G.163, P.164 Ligands: CLA.12, CLA.14, BCR.28 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.69, B:V.71, B:W.91, B:V.96, B:A.99, B:V.102, B:L.106, B:F.156, B:F.162 CLA.16: 18 residues within 4Å: Chain B: W.33, M.37, Y.40, Q.58, G.59, F.61, L.324, T.327, G.328, P.447, W.450 Chain D: F.196 Chain J: F.31, F.35 Ligands: CLA.13, CLA.22, BCR.26, BCR.27 11 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D, 2 interactions with chain J, Hydrophobic interactions: B:W.33, B:F.61, B:F.61, B:F.61, B:P.447, B:W.450, D:F.196, J:F.31, J:F.35 Hydrogen bonds: B:G.328 pi-Stacking: B:F.61 CLA.17: 18 residues within 4Å: Chain B: T.236, S.239, S.240, A.243, F.246, F.463, H.466, T.473, L.474 Chain D: F.120, M.126, L.127, F.130 Chain G: L.39, L.43 Ligands: CLA.18, CLA.19, CLA.55 10 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D, 2 interactions with chain G, Hydrophobic interactions: B:F.246, B:F.463, B:L.474, D:F.120, D:F.130, D:F.130, G:L.39, G:L.43 pi-Cation interactions: B:H.466 Metal complexes: B:H.466 CLA.18: 16 residues within 4Å: Chain B: F.139, V.208, A.212, F.215, H.216, P.221, L.225, L.229 Chain G: T.27, M.31, F.34 Ligands: CLA.12, CLA.14, CLA.17, CLA.19, BCR.58 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain G, Hydrophobic interactions: B:F.139, B:F.139, B:V.208, B:F.215, B:L.229, G:M.31, G:F.34, G:F.34 CLA.19: 17 residues within 4Å: Chain B: L.135, M.138, F.139, H.142, L.143, L.145, A.146, I.234, V.237, S.240, V.245 Ligands: CLA.13, CLA.14, CLA.17, CLA.18, CLA.21, CLA.24 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:M.138, B:F.139, B:L.145, B:A.146, B:I.234 CLA.20: 19 residues within 4Å: Chain B: W.5, Y.6, R.7, V.8, H.9, L.238, L.461, F.462, G.465, W.468, H.469, R.472 Chain R: N.12 Ligands: CLA.13, CLA.21, CLA.22, CLA.23, BCR.27, LMG.49 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:W.5, B:H.9, B:L.238, B:L.238, B:F.462, B:F.462, B:W.468 Salt bridges: B:H.9, B:R.472 pi-Stacking: B:W.468 Metal complexes: B:H.469 CLA.21: 17 residues within 4Å: Chain B: H.9, L.12, L.19, A.22, H.23, H.26, T.27, I.234, V.237, L.238, S.241 Ligands: CLA.13, CLA.14, CLA.19, CLA.20, CLA.22, CLA.24 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.12, B:L.19, B:A.22, B:H.26, B:I.234, B:L.238 Hydrogen bonds: B:S.241 Salt bridges: B:H.23 pi-Stacking: B:H.23 CLA.22: 14 residues within 4Å: Chain B: H.9, H.26, V.30, W.33, F.462 Chain K: F.14 Ligands: CLA.13, CLA.16, CLA.20, CLA.21, CLA.23, BCR.26, BCR.27, LMG.49 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain K, Hydrophobic interactions: B:V.30, B:W.33, K:F.14 Salt bridges: B:H.9 pi-Stacking: B:H.26 CLA.23: 13 residues within 4Å: Chain B: V.8, H.9, L.12, A.22, L.29, W.115 Chain J: V.10 Chain K: F.21, L.25 Ligands: CLA.20, CLA.22, BCR.26, LMG.48 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain K, Hydrophobic interactions: B:L.12, B:A.22, B:L.29, B:W.115, K:L.25 Metal complexes: B:H.9 CLA.24: 18 residues within 4Å: Chain B: I.20, H.23, L.24, T.27, L.107, L.133, M.138, I.141, H.142, L.145 Chain G: L.11, L.14 Ligands: CLA.13, CLA.14, CLA.19, CLA.21, CLA.25, BCR.28 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain G, Hydrophobic interactions: B:L.107, B:L.133, B:I.141, B:L.145, G:L.11, G:L.14 CLA.25: 11 residues within 4Å: Chain B: L.24, A.110, W.113, H.114, L.122 Chain G: T.5, L.7, G.8, L.11 Ligands: CLA.24, BCR.28 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain B, Hydrophobic interactions: G:L.11, B:L.24, B:A.110, B:L.122 Hydrogen bonds: G:L.7, G:G.8 pi-Cation interactions: B:H.114 CLA.31: 18 residues within 4Å: Chain C: G.159, A.160, L.163, I.212, V.221, H.225, I.228, M.270, I.273, A.274, F.277, V.284, Y.285 Ligands: CLA.32, CLA.33, CLA.36, CLA.37, BCR.44 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.163, C:I.212, C:I.228, C:I.273, C:A.274, C:F.277, C:F.277, C:V.284, C:V.284, C:Y.285 Metal complexes: C:H.225 CLA.32: 17 residues within 4Å: Chain C: W.51, L.76, H.79, L.162, L.267, V.278, Y.285, L.414, H.418, L.421, F.425 Ligands: LMG.30, CLA.31, CLA.33, CLA.34, CLA.41, CLA.45 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:W.51, C:L.76, C:L.162, C:L.414, C:L.421, C:F.425 Hydrogen bonds: C:Y.285 Salt bridges: C:H.79, C:H.418 pi-Cation interactions: C:H.418 CLA.33: 20 residues within 4Å: Chain C: I.48, V.49, W.51, A.52, T.56, L.76, H.79, I.80, T.82, L.83, V.102, H.106, L.267 Ligands: LMG.29, CLA.31, CLA.32, CLA.37, CLA.39, CLA.41, CLA.45 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:V.49, C:A.52, C:L.76, C:H.79, C:I.80, C:L.83, C:V.102, C:L.267 Hydrogen bonds: C:T.82 Salt bridges: C:H.79 CLA.34: 12 residues within 4Å: Chain C: W.51, M.55, F.58, Q.72, G.73, I.75, W.413, L.414, S.417 Chain I: P.26 Ligands: LMG.30, CLA.32 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:W.51, C:I.75, C:I.75, C:W.413, C:W.413 CLA.35: 13 residues within 4Å: Chain A: W.131 Chain C: I.253, Y.262, G.265, A.266, M.269, L.426, H.429, L.430, A.433, R.437 Ligands: CLA.37, BCR.44 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:Y.262, C:A.266, C:M.269, C:L.426, C:A.433 Metal complexes: C:H.429 CLA.36: 14 residues within 4Å: Chain C: L.149, L.153, I.231, G.235, W.238, H.239, P.244, F.245, W.247, A.248, F.252 Ligands: CLA.31, CLA.37, BCR.44 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.149, C:L.149, C:L.153, C:I.231, C:W.247, C:A.248, C:F.252 Hydrogen bonds: C:F.245 Salt bridges: C:H.239 Metal complexes: C:H.239 CLA.37: 15 residues within 4Å: Chain C: M.145, L.149, H.152, L.156, I.228, F.252, W.254, Y.259, Y.262, M.270 Ligands: CLA.31, CLA.33, CLA.35, CLA.36, CLA.39 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.149, C:I.228, C:F.252, C:W.254, C:Y.259, C:Y.262 CLA.38: 16 residues within 4Å: Chain C: W.24, A.25, N.27, A.28, E.257, L.260, L.264, F.424, F.425, G.428, W.431, H.432, R.435 Chain I: L.33 Ligands: CLA.39, CLA.45 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain I, Hydrophobic interactions: C:N.27, C:A.28, C:L.260, C:L.260, C:L.264, C:F.425, C:F.425, C:W.431, I:L.33 Salt bridges: C:R.435 pi-Stacking: C:W.431 CLA.39: 19 residues within 4Å: Chain C: N.27, L.30, L.37, A.40, H.41, H.44, I.48, W.139, I.148, H.152, L.260, S.263, L.264, L.267 Ligands: CLA.33, CLA.37, CLA.38, CLA.41, CLA.45 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:L.30, C:L.37, C:A.40, C:W.139, C:W.139, C:I.148, C:L.260, C:L.260 Hydrogen bonds: C:S.263 Metal complexes: C:H.41 CLA.40: 25 residues within 4Å: Chain C: W.23, G.26, N.27, R.29, L.30, L.33, K.36, A.40, F.115, V.118, A.121, I.122 Chain I: F.32, L.33, A.36, F.37, W.39, Q.40, R.46 Chain N: I.35, N.45 Chain O: V.20, V.23 Ligands: BCR.43, CLA.45 16 PLIP interactions: 8 interactions with chain I, 5 interactions with chain C, 2 interactions with chain O, 1 interactions with chain N, Hydrophobic interactions: I:F.32, I:L.33, I:A.36, I:F.37, I:W.39, I:W.39, I:Q.40, C:L.30, C:K.36, C:I.122, O:V.20, O:V.23, N:I.35 pi-Stacking: I:W.39 Salt bridges: C:K.36, C:K.36 CLA.41: 16 residues within 4Å: Chain C: H.41, A.45, F.134, F.135, I.148, F.151, H.152, V.155, I.158, G.159 Ligands: LMG.29, CLA.32, CLA.33, CLA.39, CLA.42, BCR.46 3 PLIP interactions: 3 interactions with chain C, Hydrophobic interactions: C:I.148, C:I.148, C:F.151 CLA.42: 13 residues within 4Å: Chain C: L.38, V.42, V.112, G.116, Y.119, H.120, P.125, L.128, Y.131, F.134, F.135 Ligands: CLA.41, BCR.46 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:L.38, C:V.42, C:Y.119, C:L.128, C:Y.131, C:F.134, C:F.135 pi-Stacking: C:H.120, C:H.120 CLA.45: 13 residues within 4Å: Chain C: H.44, I.48, W.51, F.424, F.425 Chain I: P.29, V.30, L.33 Ligands: CLA.32, CLA.33, CLA.38, CLA.39, CLA.40 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain I, Hydrophobic interactions: C:I.48, C:W.51, C:W.51, C:F.424, C:F.425, C:F.425, I:V.30, I:V.30, I:L.33 CLA.54: 24 residues within 4Å: Chain A: M.183, F.206, Y.254 Chain D: 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.4, CLA.6, PHO.53 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:V.152, D:F.181, D:L.182, D:F.185, D:Q.186, D:T.192, D:V.201, D:V.204, D:V.204, D:L.205, D:L.279, D:L.279, A:Y.254 pi-Stacking: D:W.191, D:H.197, D:H.197 CLA.55: 21 residues within 4Å: Chain D: I.35, C.40, L.43, L.89, L.90, L.91, L.92, W.93, T.112, F.113, L.116, H.117, F.120 Chain G: V.40, L.43 Chain M: L.14, G.17, A.18, V.20 Ligands: CLA.17, BCR.58 11 PLIP interactions: 8 interactions with chain D, 1 interactions with chain M, 2 interactions with chain G, Hydrophobic interactions: D:L.43, D:W.93, D:L.116, D:F.120, D:F.120, M:V.20, G:V.40, G:L.43 Hydrogen bonds: D:L.92 Salt bridges: D:H.117 pi-Stacking: D:F.113

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

BCR.8: 16 residues within 4Å: Chain A: F.17, V.35, L.42, A.43, I.46, C.47, I.50, A.51, A.54, A.55, L.102, W.105, L.106, P.111, L.114 Ligands: LMG.59 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.17, A:V.35, A:L.42, A:L.42, A:I.46, A:I.50, A:A.51, A:L.102, A:W.105, A:L.106, A:P.111, A:L.114 BCR.26: 9 residues within 4Å: Chain B: M.25, L.29, F.108, W.115 Ligands: CLA.16, CLA.22, CLA.23, BCR.27, LMG.48 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.29, B:F.108, B:W.115, B:W.115 BCR.27: 11 residues within 4Å: Chain B: G.32, W.33, S.36, I.101, V.102, G.105 Ligands: CLA.13, CLA.16, CLA.20, CLA.22, BCR.26 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.102 BCR.28: 9 residues within 4Å: Chain B: L.106, L.109, A.110, C.112, W.113, V.116 Ligands: CLA.15, CLA.24, CLA.25 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.106, B:L.109, B:A.110, B:V.116 BCR.43: 16 residues within 4Å: Chain C: A.43, G.46, L.47, L.107, I.108, S.110, G.114 Chain I: Y.15, F.32, A.36, W.39 Chain O: L.12, W.47, V.51 Ligands: CLA.40, BCR.60 14 PLIP interactions: 5 interactions with chain I, 3 interactions with chain O, 6 interactions with chain C Hydrophobic interactions: I:Y.15, I:F.32, I:F.32, I:A.36, I:W.39, O:L.12, O:W.47, O:V.51, C:A.43, C:L.47, C:L.47, C:L.107, C:I.108, C:I.108 BCR.44: 9 residues within 4Å: Chain C: I.197, V.215, D.220, V.221, H.225, I.228 Ligands: CLA.31, CLA.35, CLA.36 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.197, C:V.215, C:I.228 BCR.46: 10 residues within 4Å: Chain C: V.104, I.108, S.109, V.112, L.113 Chain O: G.55, N.58 Ligands: LMG.29, CLA.41, CLA.42 3 PLIP interactions: 1 interactions with chain O, 2 interactions with chain C Hydrophobic interactions: O:N.58, C:I.108, C:L.113 BCR.56: 12 residues within 4Å: Chain D: Y.42, L.43, G.46, G.47, L.49, T.50 Chain F: P.29, T.30, F.33, L.34 Ligands: CLA.6, LMG.50 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:Y.42, D:L.43, D:L.49, D:L.49, D:T.50, F:P.29, F:P.29, F:L.34 BCR.58: 12 residues within 4Å: Chain G: M.31, F.34, M.35, L.37, F.38, F.41 Chain M: L.7 Ligands: CLA.10, CLA.11, CLA.12, CLA.18, CLA.55 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain M Hydrophobic interactions: G:F.34, G:F.38, G:F.38, G:F.41, G:F.41, M:L.7 BCR.60: 10 residues within 4Å: Chain I: L.25, L.31, A.34, L.35, V.38 Chain N: I.28, G.32, I.35 Chain O: V.20 Ligands: BCR.43 7 PLIP interactions: 5 interactions with chain I, 1 interactions with chain O, 1 interactions with chain N Hydrophobic interactions: I:L.25, I:L.31, I:A.34, I:L.35, I:V.38, O:V.20, N:I.28

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

LHG.9: 10 residues within 4Å: Chain A: R.140, W.142, V.145, A.146, F.273, W.284 Chain C: V.427, W.431, R.435 Chain D: N.220 11 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:V.145, A:A.146, A:F.273, A:F.273, A:W.284, C:V.427, C:W.431 Hydrogen bonds: A:R.140, C:R.435, D:N.220 Salt bridges: A:R.140

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

LMG.29: 10 residues within 4Å: Chain C: W.85, V.101, V.102, V.105, H.106, S.109 Chain O: F.59 Ligands: CLA.33, CLA.41, BCR.46 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain O Hydrophobic interactions: C:W.85, C:V.101, C:V.102, C:V.105, O:F.59 LMG.30: 7 residues within 4Å: Chain C: F.58, H.62 Chain I: D.23, V.27, L.31 Ligands: CLA.32, CLA.34 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain I Hydrogen bonds: C:H.62 Salt bridges: C:H.62 Hydrophobic interactions: I:V.27, I:L.31 LMG.48: 21 residues within 4Å: Chain B: W.5, Y.6 Chain D: R.265, W.266, F.270, F.273 Chain J: E.11, N.13, S.16, L.19, G.20, L.22, V.26 Chain K: F.21 Chain R: R.10 Ligands: CLA.5, CLA.23, BCR.26, LMG.49, LMG.51, PL9.52 11 PLIP interactions: 4 interactions with chain D, 1 interactions with chain K, 5 interactions with chain J, 1 interactions with chain B Hydrophobic interactions: D:W.266, D:F.270, K:F.21, J:L.22, J:V.26, B:W.5 Hydrogen bonds: D:R.265, D:R.265, J:E.11, J:N.13, J:S.16 LMG.49: 18 residues within 4Å: Chain B: W.5, Y.6, R.7, L.461, F.464, W.468 Chain D: Y.141, W.266, F.269, F.273 Chain J: I.24, L.27 Chain K: P.18 Chain R: E.7, R.10 Ligands: CLA.20, CLA.22, LMG.48 14 PLIP interactions: 5 interactions with chain D, 6 interactions with chain B, 2 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: D:F.269, D:F.273, D:F.273, B:W.5, B:L.461, B:F.464, B:F.464, J:I.24, J:L.27, K:P.18 Hydrogen bonds: D:Y.141, D:Y.141, B:Y.6, B:R.7 LMG.50: 10 residues within 4Å: Chain D: Y.67, C.71, N.72, F.73 Chain F: T.30, I.37, M.40, Q.41 Ligands: CLA.6, BCR.56 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:T.30 Hydrogen bonds: F:Q.41 LMG.51: 24 residues within 4Å: Chain A: L.28, 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.13, T.15, S.16, Y.18, L.19 Chain L: F.10, F.17, A.20, I.21 Ligands: CLA.4, CLA.5, LMG.48, PL9.52 19 PLIP interactions: 6 interactions with chain L, 5 interactions with chain J, 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: L:F.10, L:F.17, L:F.17, L:F.17, L:A.20, L:I.21, J:Y.18, J:L.19, D:F.257, D:F.261, D:F.270, A:L.28 Hydrogen bonds: J:N.13, J:T.15, J:S.16, D:S.262, D:S.262, D:N.263, D:N.263 LMG.59: 4 residues within 4Å: Chain H: T.3, T.7, V.11 Ligands: BCR.8 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:T.3

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

FE.47: 5 residues within 4Å: Chain A: H.215, H.272 Chain D: H.214, E.241, H.268 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Metal complexes: D:H.214, D:E.241, D:H.268, A:H.215, A:H.272

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.52, I.53, I.77 Chain D: M.199, A.202, G.203, L.209, H.214, T.217, M.246, A.249, N.250, W.253, F.257, I.259, A.260, F.261, L.267, V.274, T.277 Chain J: V.26, L.29, L.30 Chain L: F.10 Ligands: CLA.5, LMG.48, LMG.51 18 PLIP interactions: 11 interactions with chain D, 3 interactions with chain A, 2 interactions with chain J, 2 interactions with chain L Hydrophobic interactions: D:M.199, D:A.202, D:L.209, D:T.217, D:W.253, D:F.257, D:F.261, D:L.267, D:V.274, D:T.277, A:F.52, A:I.53, A:I.77, J:V.26, J:L.30, L:F.10, L:F.10 Hydrogen bonds: D:F.261

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

HEM.57: 13 residues within 4Å: Chain E: I.13, R.18, Y.19, H.23, T.26 Chain F: Y.13, P.14, I.15, R.19, W.20, H.24, A.27, I.31 9 PLIP interactions: 4 interactions with chain F, 5 interactions with chain E, Hydrophobic interactions: F:A.27, F:I.31, E:I.13, E:Y.19 pi-Stacking: F:W.20, E:H.23 Metal complexes: F:H.24 Salt bridges: E:R.18 pi-Cation interactions: E:R.18

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
Photosystem II lipoprotein Psb27: P
Photosystem II reaction center Psb28 protein: Q
Tsl0063 protein: R

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

P
1

Q
2

R
3

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

Photosystem II lipoprotein Psb27

Photosystem II reaction center Psb28 protein

Tsl0063 protein

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