SMTL ID : 7nhq.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-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, E.241, H.268 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Metal complexes: A:H.215, A:H.272, D:H.214, D:E.241, D:H.268

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

MN.2: 2 residues within 4Å: Chain A: D.170 Chain C: E.342 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.170

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

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

2 x PHO: PHEOPHYTIN A(Non-covalent)

PHO.4: 21 residues within 4Å: Chain A: L.41, A.44, T.45, F.48, F.119, Y.126, Q.130, A.146, Y.147, A.149, P.150, L.174, G.175 Chain D: L.205, L.209, I.213, W.253 Ligands: CLA.5, CLA.46, LMG.49, PL9.50 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:L.41, A:A.44, A:F.48, A:F.119, A:Y.147, A:A.149, A:L.174, D:L.205, D:L.209, D:I.213 Hydrogen bonds: A:Y.126, A:Q.130, A:Y.147 PHO.51: 21 residues within 4Å: Chain A: A.209, L.210, M.214, Y.254, F.255 Chain D: A.41, A.44, W.48, G.118, L.122, F.125, Q.129, A.145, F.146, P.149, F.173, G.174, P.275, L.279 Ligands: CLA.47, CLA.52 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain D Hydrophobic interactions: A:L.210, D:A.41, D:A.44, D:W.48, D:W.48, D:L.122, D:A.145, D:P.149, D:F.173, D:P.275, D:L.279 Hydrogen bonds: A:Y.254, D:Q.129 pi-Stacking: D:F.146

35 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.5: 24 residues within 4Å: Chain A: F.119, P.150, S.153, A.154, F.182, M.183, F.186, Q.187, L.193, H.198, G.201, V.202, F.206, V.283, T.286, I.290 Chain D: L.182, F.257 Chain L: F.17 Ligands: PHO.4, CLA.46, CLA.47, LMG.49, CLA.52 12 PLIP interactions: 9 interactions with chain A, 2 interactions with chain D, 1 interactions with chain L, Hydrophobic interactions: A:F.119, A:F.182, A:F.186, A:Q.187, A:L.193, A:F.206, A:V.283, A:T.286, D:L.182, D:F.257, L:F.17 Metal complexes: A:H.198 CLA.6: 19 residues within 4Å: Chain A: I.36, P.39, T.40, F.93, Y.94, P.95, I.96, W.97, L.114, F.117, H.118, L.121 Chain C: F.206 Chain H: V.8, Y.9, V.12, F.15 Ligands: BCR.7, CLA.34 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain H, Hydrophobic interactions: A:I.36, A:T.40, A:I.96, A:L.114, A:F.117, A:L.121, H:V.8, H:Y.9, H:Y.9, H:V.12, H:V.12, H:F.15, H:F.15, H:F.15 Hydrogen bonds: A:I.96 pi-Cation interactions: A:H.118 CLA.9: 12 residues within 4Å: Chain B: W.185, G.186, P.187, F.190, I.203, A.204 Chain G: F.41, I.44 Chain Q: A.52, V.53 Ligands: CLA.10, BCR.57 8 PLIP interactions: 4 interactions with chain B, 3 interactions with chain G, 1 interactions with chain Q, Hydrophobic interactions: B:W.185, B:F.190, B:I.203, B:A.204, G:F.41, G:F.41, G:I.44, Q:A.52 CLA.10: 20 residues within 4Å: Chain B: W.185, G.189, F.190, P.192, G.197, V.198, H.201, V.208, F.250, V.251, G.254, Y.258, S.260 Chain D: L.162 Chain G: F.41, I.45, Y.49 Ligands: CLA.9, CLA.11, BCR.57 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain G, Hydrophobic interactions: B:F.190, B:F.190, B:H.201, B:V.208, B:V.251, G:F.41, G:Y.49 Hydrogen bonds: B:S.260 Metal complexes: B:H.201 pi-Stacking: G:F.41 CLA.11: 22 residues within 4Å: Chain B: L.69, A.146, L.149, F.153, M.166, V.198, H.201, H.202, A.205, F.247, A.248, V.251, V.252, T.255, T.262 Chain G: F.38 Ligands: CLA.10, CLA.12, CLA.13, CLA.14, CLA.16, CLA.17 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: B:L.149, B:F.153, B:F.153, B:A.205, B:F.247, B:A.248, B:V.251, B:V.252, B:T.262, G:F.38 Hydrogen bonds: B:T.262 Salt bridges: B:H.202 pi-Stacking: B:F.153 Metal complexes: B:H.202 CLA.12: 22 residues within 4Å: Chain B: W.33, F.65, R.68, L.145, V.245, A.248, A.249, V.252, F.451, H.455, F.458, F.462 Ligands: CLA.11, CLA.13, CLA.14, CLA.15, CLA.19, CLA.20, CLA.21, CLA.23, BCR.26, BCR.27 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.33, B:F.65, B:F.65, B:L.145, B:V.245, B:A.248, B:A.249, B:F.458, B:F.458, B:F.462, B:F.462, B:F.462 pi-Stacking: B:F.451 Metal complexes: B:H.455 CLA.13: 21 residues within 4Å: Chain B: T.27, V.30, A.31, A.34, A.38, F.65, M.66, R.68, L.69, V.96, H.100, L.103, L.143, A.146 Ligands: CLA.11, CLA.12, CLA.14, CLA.18, CLA.20, CLA.23, BCR.27 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:T.27, B:A.31, B:A.34, B:V.96, B:L.103, B:L.143, B:A.146 Salt bridges: B:H.100 CLA.14: 19 residues within 4Å: Chain B: L.69, G.70, V.71, W.91, V.96, A.99, L.103, L.106, L.149, G.152, F.153, F.156, H.157, F.162, P.164 Ligands: CLA.11, CLA.12, CLA.13, CLA.24 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.69, B:V.71, B:W.91, B:V.96, B:L.103, B:L.106, B:L.149, B:F.153, B:F.156, B:F.162 pi-Stacking: B:F.153, B:H.157 CLA.15: 19 residues within 4Å: Chain B: W.33, M.37, E.41, Q.58, G.59, F.61, L.324, F.325, T.327, G.328, P.329, P.447, W.450, A.454 Chain J: F.31 Chain K: F.14 Ligands: CLA.12, CLA.21, BCR.26 12 PLIP interactions: 10 interactions with chain B, 1 interactions with chain J, 1 interactions with chain K, Hydrophobic interactions: B:W.33, B:F.61, B:T.327, B:P.447, B:W.450, B:W.450, B:A.454, J:F.31, K:F.14 Hydrogen bonds: B:E.41, B:G.328 pi-Stacking: B:F.61 CLA.16: 17 residues within 4Å: Chain B: L.229, T.236, S.239, S.240, A.243, F.463, H.466, L.474 Chain D: F.120, I.123, M.126, L.127, F.130 Ligands: CLA.11, CLA.17, CLA.18, CLA.53 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain D, Hydrophobic interactions: B:L.229, B:A.243, B:F.463, B:L.474, B:L.474, D:F.120, D:I.123, D:L.127, D:L.127, D:F.130 Salt bridges: B:H.466 pi-Stacking: B:H.466 Metal complexes: B:H.466 CLA.17: 20 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, M.231 Chain G: T.27, L.30, M.31, F.34, M.35 Ligands: CLA.11, CLA.16, CLA.18, BCR.57 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain G, Hydrophobic interactions: B:F.139, B:F.139, B:V.208, B:A.212, B:F.215, B:L.225, B:L.229, G:L.30, G:F.34, G:F.34 Salt bridges: B:H.216 pi-Stacking: B:H.216 CLA.18: 17 residues within 4Å: Chain B: L.135, M.138, F.139, H.142, L.143, L.145, A.146, M.231, I.234, T.236, V.237, S.240 Ligands: CLA.13, CLA.16, CLA.17, CLA.20, CLA.23 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:L.135, B:L.135, B:F.139, B:L.145, B:A.146, B:I.234, B:T.236, B:V.237 Hydrogen bonds: B:H.142 CLA.19: 19 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, G.465, W.468, H.469, R.472 Ligands: CLA.12, CLA.20, CLA.21, LMG.48, LMG.60 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:W.5, B:H.9, B:T.10, B:L.238, B:I.242, B:F.462, B:W.468 Salt bridges: B:H.9, B:R.472 Metal complexes: B:H.469 CLA.20: 18 residues within 4Å: Chain B: H.9, L.12, I.13, L.19, A.22, H.23, H.26, I.234, V.237, L.238, S.241, I.242 Ligands: CLA.12, CLA.13, CLA.18, CLA.19, CLA.21, CLA.22 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:H.9, B:L.12, B:I.13, B:L.19, B:A.22, B:H.26, B:I.234, B:V.237 Hydrogen bonds: B:S.241 Metal complexes: B:H.23 CLA.21: 14 residues within 4Å: Chain B: H.26, L.29, V.30, W.33, F.458, L.461, F.462 Chain K: F.14 Ligands: CLA.12, CLA.15, CLA.19, CLA.20, CLA.22, LMG.48 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain K, Hydrophobic interactions: B:L.29, B:V.30, B:W.33, B:F.458, B:F.458, B:L.461, B:F.462, B:F.462, K:F.14 pi-Stacking: B:H.26 Metal complexes: B:H.26 CLA.22: 15 residues within 4Å: Chain B: L.3, V.8, H.9, V.11, L.12, M.25, W.115 Chain J: Q.8, V.10 Chain K: F.21, L.25 Ligands: CLA.20, CLA.21, BCR.25, LMG.60 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain K, Hydrophobic interactions: B:V.11, B:L.12, B:M.25, B:W.115, B:W.115, B:W.115, K:F.21, K:L.25 pi-Cation interactions: B:H.9 Metal complexes: B:H.9 CLA.23: 15 residues within 4Å: Chain B: I.20, H.23, L.24, L.107, M.138, I.141, H.142, L.145 Chain G: L.14, N.15 Ligands: CLA.12, CLA.13, CLA.18, CLA.24, BCR.27 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain G, Hydrophobic interactions: B:I.141, B:L.145, G:L.14, G:L.14 pi-Stacking: B:H.142 Metal complexes: B:H.142 CLA.24: 11 residues within 4Å: Chain B: L.24, A.110, W.113, H.114, L.120, F.123 Chain G: T.5, L.11 Ligands: CLA.14, CLA.23, BCR.27 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: B:L.24, B:L.120, B:F.123, G:L.11 pi-Stacking: B:W.113 Metal complexes: B:H.114 CLA.30: 14 residues within 4Å: Chain C: A.160, L.163, V.221, H.225, I.228, M.270, I.273, F.277, V.284, Y.285 Ligands: CLA.31, CLA.32, CLA.36, BCR.43 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:A.160, C:L.163, C:V.221, C:I.228, C:I.228, C:M.270, C:I.273, C:I.273, C:F.277, C:F.277, C:V.284 Salt bridges: C:H.225 Metal complexes: C:H.225 CLA.31: 17 residues within 4Å: Chain C: W.51, H.79, W.85, L.162, L.163, F.170, L.267, M.270, A.274, V.278, Y.285, L.414, H.418, F.425 Ligands: CLA.30, CLA.32, CLA.44 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:W.51, C:W.85, C:W.85, C:F.170, C:L.414, C:F.425 Salt bridges: C:H.418 CLA.32: 15 residues within 4Å: Chain C: I.48, W.51, A.52, L.76, H.79, I.80, L.83, V.102, H.106, L.267, M.270 Ligands: LMG.28, CLA.30, CLA.31, CLA.44 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:A.52, C:H.79, C:I.80, C:V.102, C:L.267 Salt bridges: C:H.79, C:H.106 CLA.33: 11 residues within 4Å: Chain C: W.51, M.55, G.73, I.75, L.392, S.394, W.413, S.417 Chain I: P.26, V.30 Ligands: LMG.29 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain I, Hydrophobic interactions: C:I.75, C:W.413, C:W.413, C:W.413, I:V.30 pi-Stacking: C:W.413 CLA.34: 15 residues within 4Å: Chain A: W.131 Chain C: I.253, Y.262, G.265, A.266, M.269, H.429, L.430, A.433, R.437 Chain H: V.16, F.19 Ligands: CLA.6, CLA.36, BCR.43 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain H, Hydrophobic interactions: C:Y.262, C:Y.262, C:A.266, C:M.269, C:L.430, H:V.16, H:F.19 Hydrogen bonds: C:Y.262 pi-Stacking: C:H.429 Metal complexes: C:H.429 CLA.35: 14 residues within 4Å: Chain C: L.149, W.211, I.231, G.235, W.238, H.239, T.242, P.244, F.245, W.247, A.248, F.252 Ligands: CLA.36, BCR.43 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.149, C:W.211, C:A.248, C:F.252 Hydrogen bonds: C:F.245 CLA.36: 16 residues within 4Å: Chain C: L.149, H.152, L.153, L.156, I.231, C.232, F.252, W.254, Y.259, Y.262, A.266 Ligands: CLA.30, CLA.34, CLA.35, CLA.38, BCR.43 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:L.149, C:I.231, C:F.252, C:F.252, C:W.254, C:Y.259, C:Y.262, C:A.266 CLA.37: 16 residues within 4Å: Chain C: W.24, A.25, N.27, A.28, L.260, L.264, F.424, F.425, G.428, W.431, H.432, R.435 Ligands: LHG.8, CLA.38, CLA.39, CLA.44 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:N.27, C:A.28, C:L.260, C:L.260, C:L.264, C:F.424, C:F.425, C:F.425 Salt bridges: C:H.432, C:R.435 CLA.38: 16 residues within 4Å: Chain C: N.27, L.30, L.37, A.40, H.41, H.44, Y.137, L.260, S.263, L.264, L.267 Ligands: CLA.36, CLA.37, CLA.39, CLA.40, CLA.44 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:L.30, C:L.37, C:A.40, C:H.44, C:Y.137 Hydrogen bonds: C:S.263 pi-Stacking: C:H.41 Metal complexes: C:H.41 CLA.39: 27 residues within 4Å: Chain C: R.14, W.23, G.26, N.27, R.29, L.30, L.33, K.36, A.40, G.114, F.115, A.121 Chain I: F.32, L.33, L.35, A.36, F.37, W.39, Q.40, R.46 Chain N: I.35 Chain O: V.20, P.24 Ligands: CLA.37, CLA.38, BCR.42, CLA.44 12 PLIP interactions: 6 interactions with chain I, 2 interactions with chain O, 4 interactions with chain C, Hydrophobic interactions: I:F.32, I:L.33, I:F.37, I:F.37, I:Q.40, O:P.24, O:P.24, C:W.23, C:L.30, C:K.36 pi-Stacking: I:W.39 Salt bridges: C:K.36 CLA.40: 14 residues within 4Å: Chain C: H.41, V.42, L.113, L.128, F.134, F.135, Y.137, I.148, F.151, H.152, V.155 Ligands: CLA.38, CLA.41, BCR.45 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:H.41, C:L.128, C:Y.137, C:I.148, C:F.151, C:V.155, C:V.155 Hydrogen bonds: C:H.41 Metal complexes: C:H.152 CLA.41: 10 residues within 4Å: Chain C: L.38, V.112, G.116, Y.119, H.120, L.128, Y.131, F.135 Ligands: CLA.40, BCR.45 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.38, C:V.112, C:L.128, C:F.135, C:F.135 CLA.44: 15 residues within 4Å: Chain C: H.44, L.47, I.48, W.51, L.421, F.424, F.425 Chain I: P.29, V.30, L.33 Ligands: CLA.31, CLA.32, CLA.37, CLA.38, CLA.39 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain I, Hydrophobic interactions: C:L.47, C:I.48, C:W.51, C:W.51, C:L.421, C:F.424, C:F.425, C:F.425, I:P.29, I:V.30, I:V.30, I:L.33 pi-Stacking: C:H.44 CLA.46: 16 residues within 4Å: Chain A: F.158, M.172, I.176, T.179, F.180, F.182, M.183 Chain D: M.198, V.201, A.202 Ligands: PHO.4, CLA.5, LMG.49, PL9.50, CLA.52, LMG.60 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:F.158, A:T.179, A:F.180, A:F.182 CLA.47: 15 residues within 4Å: Chain A: Q.199, V.202, A.203, L.210, F.211, W.278 Chain D: F.153, F.157, V.175, I.178, F.179, L.182 Ligands: CLA.5, PHO.51, CLA.52 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D, Hydrophobic interactions: A:V.202, A:A.203, A:F.211, A:W.278, D:F.153, D:F.157, D:I.178, D:L.182 CLA.52: 23 residues within 4Å: Chain A: M.183, F.206 Chain D: P.149, V.152, S.155, V.156, F.181, L.182, F.185, W.191, T.192, H.197, G.200, V.201, V.204, L.279, S.282, A.283, V.286 Ligands: CLA.5, CLA.46, CLA.47, PHO.51 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:V.152, D:V.152, D:F.181, D:L.182, D:F.185, D:T.192, D:V.201, D:V.204, D:V.204, D:L.279 pi-Stacking: D:W.191 pi-Cation interactions: D:H.197 Metal complexes: D:H.197 CLA.53: 22 residues within 4Å: Chain D: P.39, 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.33, L.39, L.43 Chain M: L.14, G.17, A.18, V.20 Ligands: CLA.16, BCR.56 15 PLIP interactions: 9 interactions with chain D, 2 interactions with chain M, 4 interactions with chain G, Hydrophobic interactions: D:P.39, D:L.43, D:W.93, D:W.93, D:L.116, D:F.120, M:A.18, M:V.20, G:V.33, G:L.39, G:L.43, G:L.43 Hydrogen bonds: D:L.92 pi-Stacking: D:F.113, D:H.117

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

BCR.7: 9 residues within 4Å: Chain A: P.39, L.42, A.43, A.51, A.54, A.55, L.106, P.111 Ligands: CLA.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.39, A:L.42, A:A.51, A:L.106, A:L.106, A:P.111 BCR.25: 6 residues within 4Å: Chain B: M.25, L.29, F.108, W.115 Ligands: CLA.22, BCR.26 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.29, B:F.108, B:W.115, B:W.115 BCR.26: 11 residues within 4Å: Chain B: L.29, G.32, W.33, I.101, V.102, S.104, G.105, L.109 Ligands: CLA.12, CLA.15, BCR.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.29, B:L.109 BCR.27: 10 residues within 4Å: Chain B: L.103, L.106, L.109, A.110, C.112, W.113 Ligands: CLA.12, CLA.13, CLA.23, CLA.24 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.103, B:L.106, B:L.109, B:A.110, B:W.113 BCR.42: 22 residues within 4Å: Chain C: A.43, G.46, L.47, F.50, L.107, I.108, S.110, A.111, G.114, V.118 Chain I: Y.15, F.32, L.35, A.36, W.39 Chain O: L.9, L.12, S.16, W.47, V.51 Ligands: CLA.39, BCR.59 14 PLIP interactions: 6 interactions with chain I, 4 interactions with chain O, 4 interactions with chain C Hydrophobic interactions: I:Y.15, I:F.32, I:F.32, I:L.35, I:A.36, I:W.39, O:L.9, O:L.12, O:W.47, O:V.51, C:L.47, C:L.47, C:A.111, C:V.118 BCR.43: 12 residues within 4Å: Chain C: I.197, Y.200, L.201, I.212, V.215, G.224, I.228, M.269 Ligands: CLA.30, CLA.34, CLA.35, CLA.36 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.200, C:L.201, C:I.212, C:V.215, C:I.228 BCR.45: 10 residues within 4Å: Chain C: V.101, V.104, V.105, I.108, V.112, L.113 Chain O: G.55, F.59 Ligands: CLA.40, CLA.41 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain O Hydrophobic interactions: C:V.101, C:I.108, C:V.112, C:L.113, O:F.59, O:F.59 BCR.56: 10 residues within 4Å: Chain D: Y.42, G.46, L.49, W.104, F.113 Chain F: P.29, T.30, F.33 Ligands: CLA.53, LMG.55 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:L.49, D:W.104, D:F.113, D:F.113, F:P.29, F:F.33, F:F.33 BCR.57: 10 residues within 4Å: Chain G: F.34, M.35, L.37, F.38, F.41 Chain M: L.7, F.11 Ligands: CLA.9, CLA.10, CLA.17 8 PLIP interactions: 6 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:F.41, M:L.7, M:F.11 BCR.59: 9 residues within 4Å: Chain I: L.25, A.34, F.37 Chain N: I.28, G.32 Chain O: S.16, V.20 Ligands: LMG.29, BCR.42 7 PLIP interactions: 2 interactions with chain O, 3 interactions with chain I, 2 interactions with chain N Hydrophobic interactions: O:V.20, O:V.20, I:L.25, I:A.34, I:F.37, N:I.28, N:I.28

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

LHG.8: 12 residues within 4Å: Chain A: R.140, W.142, A.146, Y.262, F.273, A.276, W.278 Chain C: W.431, R.435 Chain D: A.216, N.220 Ligands: CLA.37 11 PLIP interactions: 2 interactions with chain C, 7 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: C:W.431, A:A.146, A:F.273, A:A.276, A:W.278, D:A.216 Hydrogen bonds: C:R.435, A:R.140, D:N.220 Salt bridges: A:R.140, A:R.269

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

LMG.28: 10 residues within 4Å: Chain C: W.85, D.95, F.97, P.98, V.101, V.102, H.106, S.109 Chain O: F.59 Ligands: CLA.32 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain O Hydrophobic interactions: C:W.85, C:W.85, C:P.98, C:V.101, C:V.102 Hydrogen bonds: O:F.59 LMG.29: 7 residues within 4Å: Chain C: F.58, H.62, S.417 Chain I: D.23, V.24 Ligands: CLA.33, BCR.59 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: I:V.24 Hydrogen bonds: C:H.62 LMG.48: 15 residues within 4Å: Chain B: Y.6, R.7, L.461, F.464, W.468 Chain D: Y.141, F.269, F.273, W.280, M.281 Chain J: I.24, L.27 Ligands: CLA.19, CLA.21, LMG.60 8 PLIP interactions: 2 interactions with chain J, 2 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: J:I.24, J:L.27, B:L.461, D:F.273, D:W.280 Hydrogen bonds: B:R.7, D:Y.141, D:Y.141 LMG.49: 27 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, L.22 Chain L: F.10, I.13, F.17, A.20, I.21 Ligands: PHO.4, CLA.5, CLA.46, PL9.50, LMG.60 19 PLIP interactions: 7 interactions with chain J, 6 interactions with chain L, 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: J:Y.18, J:L.19, J:L.19, J:L.22, L:I.13, L:F.17, L:F.17, L:F.17, L:A.20, L:I.21, 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 LMG.55: 11 residues within 4Å: Chain D: L.49, Y.67, C.71, N.72, F.73 Chain F: L.26, T.30, I.37, M.40, Q.41 Ligands: BCR.56 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:M.40, F:Q.41 Hydrophobic interactions: D:L.49, D:F.73, D:F.73 LMG.58: 6 residues within 4Å: Chain H: M.1, T.3, T.7, I.10, V.11, F.14 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:I.10, H:V.11, H:V.11, H:F.14 Hydrogen bonds: H:M.1 LMG.60: 22 residues within 4Å: Chain B: W.5, Y.6 Chain D: R.265, W.266, F.273 Chain J: E.11, N.13, S.16, L.19, G.20, L.22, L.23, V.26 Chain K: P.18, F.21 Chain Q: R.10 Ligands: CLA.19, CLA.22, CLA.46, LMG.48, LMG.49, PL9.50 15 PLIP interactions: 6 interactions with chain J, 2 interactions with chain Q, 3 interactions with chain K, 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: J:L.19, J:L.22, J:L.23, K:P.18, K:F.21, K:F.21, D:W.266, B:W.5, B:W.5 Hydrogen bonds: J:E.11, J:N.13, J:S.16, Q:R.10, Q:R.10, D:R.265

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)

PL9.50: 26 residues within 4Å: Chain A: F.52 Chain D: M.199, A.202, G.203, L.209, I.213, H.214, T.217, M.246, N.250, W.253, F.257, I.259, A.260, F.261, L.267, F.273, V.274, T.277 Chain J: V.26, L.29, L.30 Ligands: PHO.4, CLA.46, LMG.49, LMG.60 19 PLIP interactions: 15 interactions with chain D, 2 interactions with chain J, 2 interactions with chain A Hydrophobic interactions: D:M.199, D:A.202, D:L.209, D:I.213, D:W.253, D:F.257, D:I.259, D:F.261, D:L.267, D:F.273, D:V.274, D:T.277, J:V.26, J:L.29, A:F.52, A:F.52 Hydrogen bonds: D:H.214, D:T.217, D:F.261

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

HEM.54: 12 residues within 4Å: Chain E: R.8, I.13, R.18, I.22, H.23, I.27 Chain F: I.15, W.20, V.23, H.24, A.27, I.31 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain F, Hydrophobic interactions: E:R.18, E:I.22, E:I.27, F:V.23, F:V.23, F:A.27 Salt bridges: E:R.8 Metal complexes: E:H.23, 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
Photosystem II reaction center Psb28 protein: P
Tsl0063 protein: Q

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
2

Q
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 reaction center Psb28 protein

Tsl0063 protein

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