SMTL ID : 7dxa.1

PSII intermediate Psb28-RC47

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

SQD.1: 5 residues within 4Å: Chain C: R.16, W.20, L.28, V.30 Chain L: F.22 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.30 Hydrogen bonds: C:R.16 SQD.47: 11 residues within 4Å: Chain J: R.14, L.17, Y.18, L.21 Chain K: I.23, Y.26, V.27, E.30 Chain L: L.16, F.19 Ligands: MGE.48 12 PLIP interactions: 2 interactions with chain L, 6 interactions with chain K, 4 interactions with chain J Hydrophobic interactions: L:L.16, L:F.19, K:I.23, K:I.23, K:Y.26, K:Y.26, K:V.27, K:E.30, J:L.17, J:L.21 Salt bridges: J:R.14, J:R.14

22 x CLA: CHLOROPHYLL A(Non-covalent)

CLA.2: 24 residues within 4Å: Chain C: F.119, Y.147, P.150, S.153, V.157, M.183, F.186, Q.187, I.192, L.193, H.198, G.201, V.202, F.206, V.283, A.286, A.287 Chain E: L.172, L.195 Chain L: F.17 Ligands: CLA.3, PHO.4, CLA.33, CLA.36 16 PLIP interactions: 12 interactions with chain C, 3 interactions with chain E, 1 interactions with chain L, Hydrophobic interactions: C:F.119, C:F.119, C:F.186, C:Q.187, C:I.192, C:I.192, C:L.193, C:V.202, C:V.202, C:F.206, C:F.206, E:L.172, E:L.172, E:L.195, L:F.17 Metal complexes: C:H.198 CLA.3: 16 residues within 4Å: Chain C: Q.199, V.202, A.203, F.206, G.207, L.210, W.278 Chain E: L.64, F.147, V.165, I.168, F.169, L.172 Ligands: CLA.2, PHO.5, CLA.36 12 PLIP interactions: 7 interactions with chain E, 5 interactions with chain C, Hydrophobic interactions: E:F.147, E:F.147, E:I.168, E:I.168, E:F.169, E:L.172, E:L.172, C:V.202, C:F.206, C:L.210, C:W.278 pi-Stacking: C:F.206 CLA.6: 18 residues within 4Å: Chain C: I.36, P.39, T.40, F.93, Y.94, P.95, I.96, W.97, L.114, H.118, L.121 Chain I: V.8, Y.9, V.11, V.12, F.15 Ligands: BCR.7, MGE.9 15 PLIP interactions: 6 interactions with chain I, 9 interactions with chain C, Hydrophobic interactions: I:Y.9, I:V.11, I:V.12, I:V.12, I:F.15, I:F.15, C:T.40, C:P.95, C:I.96, C:W.97, C:L.121 Hydrogen bonds: C:I.96 Salt bridges: C:H.118 pi-Cation interactions: C:H.118, C:H.118 CLA.10: 6 residues within 4Å: Chain D: G.185, P.186, F.189 Chain H: F.40 Ligands: CLA.11, BCR.46 1 PLIP interactions: 1 interactions with chain D, Hydrophobic interactions: D:P.186 CLA.11: 21 residues within 4Å: Chain D: G.188, F.189, P.191, G.196, A.199, H.200, A.203, V.207, F.246, F.249 Chain H: F.37, F.40, I.44, L.45, Y.48 Ligands: CLA.10, CLA.12, CLA.14, CLA.18, DGD.44, BCR.46 13 PLIP interactions: 6 interactions with chain H, 7 interactions with chain D, Hydrophobic interactions: H:F.37, H:F.40, H:I.44, H:I.44, H:L.45, D:A.199, D:H.200, D:V.207, D:V.207, D:F.246, D:F.246, D:F.249 pi-Stacking: H:F.40 CLA.12: 27 residues within 4Å: Chain D: R.67, L.68, A.145, C.149, F.152, M.165, V.197, H.200, H.201, A.243, F.246, A.247, V.250, V.251, T.261 Chain H: M.34, F.37, L.38, L.41 Ligands: CLA.11, CLA.13, CLA.14, CLA.15, CLA.17, CLA.18, CLA.19, BCR.46 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain H, Hydrophobic interactions: D:A.145, D:F.152, D:F.152, D:F.152, D:V.197, D:A.243, D:F.246, D:F.246, D:A.247, D:V.250, H:F.37, H:L.38 Hydrogen bonds: D:R.67 Salt bridges: D:R.67 pi-Stacking: D:H.200 CLA.13: 24 residues within 4Å: Chain D: W.32, F.60, F.64, R.67, L.144, L.147, L.148, V.244, A.247, A.248, V.251, F.450, H.454, F.457, F.461 Ligands: CLA.12, CLA.14, CLA.15, CLA.16, CLA.20, CLA.21, CLA.22, CLA.24, BCR.27 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:W.32, D:F.60, D:F.64, D:L.147, D:L.147, D:V.244, D:A.247, D:V.251, D:F.457, D:F.457, D:F.461, D:F.461 Salt bridges: D:R.67 CLA.14: 26 residues within 4Å: Chain D: T.26, V.29, A.30, W.32, A.33, A.37, V.61, F.64, M.65, R.67, H.99, L.102, L.142, A.145, G.146, C.149, A.204 Ligands: CLA.11, CLA.12, CLA.13, CLA.15, CLA.18, CLA.19, CLA.21, CLA.24, BCR.28 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:T.26, D:V.29, D:W.32, D:A.33, D:L.102, D:L.142, D:A.145 Salt bridges: D:R.67 CLA.15: 21 residues within 4Å: Chain D: L.68, G.69, F.89, W.90, V.95, A.98, H.99, V.101, L.102, L.148, G.151, F.152, F.155, H.156, F.161, G.162, P.163 Ligands: CLA.12, CLA.13, CLA.14, BCR.28 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:L.68, D:L.68, D:F.89, D:F.89, D:F.89, D:W.90, D:W.90, D:W.90, D:A.98, D:L.148, D:F.155, D:F.161 Salt bridges: D:H.99 pi-Stacking: D:W.90 CLA.16: 25 residues within 4Å: Chain D: W.32, M.36, Y.39, Q.57, G.58, F.60, L.323, F.324, T.326, G.327, P.328, W.449, F.450, A.453, H.454 Chain E: T.267, M.271 Chain J: F.35 Chain K: F.14 Ligands: CLA.13, CLA.22, BCR.26, BCR.27, MGE.29, MGE.41 11 PLIP interactions: 8 interactions with chain D, 1 interactions with chain J, 1 interactions with chain E, 1 interactions with chain K, Hydrophobic interactions: D:Y.39, D:F.60, D:F.60, D:F.324, D:W.449, J:F.35, E:T.267, K:F.14 Hydrogen bonds: D:Y.39, D:G.327 pi-Stacking: D:F.60 CLA.17: 23 residues within 4Å: Chain D: L.228, T.235, S.238, S.239, A.242, F.246, F.462, H.465, G.469, L.473 Chain E: L.26, L.79, F.110, I.113, M.116, L.117, I.140 Ligands: CLA.12, CLA.18, CLA.19, UNL.30, CLA.37, DGD.44 16 PLIP interactions: 9 interactions with chain E, 7 interactions with chain D, Hydrophobic interactions: E:L.26, E:L.79, E:F.110, E:F.110, E:I.113, E:I.113, E:M.116, E:L.117, E:I.140, D:F.246, D:F.462, D:F.462, D:L.473 Hydrogen bonds: D:S.238 Salt bridges: D:H.465 pi-Stacking: D:H.465 CLA.18: 26 residues within 4Å: Chain D: F.138, L.142, V.207, A.211, F.214, H.215, V.218, R.219, P.220, P.221, L.224, L.228 Chain H: T.26, M.30, F.33, M.34, L.38, L.41, L.42, L.45 Ligands: CLA.11, CLA.12, CLA.14, CLA.17, CLA.19, BCR.46 16 PLIP interactions: 7 interactions with chain H, 9 interactions with chain D, Hydrophobic interactions: H:M.30, H:F.33, H:L.38, H:L.41, H:L.42, H:L.45, D:F.138, D:F.138, D:F.138, D:L.142, D:V.207, D:A.211, D:F.214, D:F.214, D:L.228 Hydrogen bonds: H:T.26 CLA.19: 21 residues within 4Å: Chain D: L.134, M.137, F.138, H.141, L.142, L.144, A.145, L.228, M.230, I.233, T.235, V.236, S.239, S.240, A.243 Ligands: CLA.12, CLA.14, CLA.17, CLA.18, CLA.21, CLA.24 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:L.134, D:M.137, D:F.138, D:L.144, D:M.230, D:I.233, D:T.235, D:V.236 CLA.20: 23 residues within 4Å: Chain B: N.12 Chain D: W.4, Y.5, R.6, V.7, H.8, T.9, L.237, I.241, F.457, L.460, F.461, F.463, G.464, W.467, H.468, R.471 Chain K: F.21 Ligands: CLA.13, CLA.21, CLA.22, CLA.23, MGE.41 14 PLIP interactions: 1 interactions with chain K, 13 interactions with chain D, Hydrophobic interactions: K:F.21, D:H.8, D:T.9, D:L.237, D:I.241, D:F.457, D:F.461, D:F.461, D:F.463 Hydrogen bonds: D:V.7, D:H.8 Salt bridges: D:H.8, D:R.471 pi-Stacking: D:W.467 CLA.21: 21 residues within 4Å: Chain D: H.8, L.11, I.12, L.18, A.21, H.22, H.25, T.26, I.233, V.236, L.237, S.240, I.241, V.244 Ligands: CLA.13, CLA.14, CLA.19, CLA.20, CLA.22, CLA.23, CLA.24 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:H.8, D:L.11, D:I.12, D:L.18, D:A.21, D:H.22, D:T.26, D:I.233, D:I.233, D:V.236, D:L.237, D:L.237, D:V.244 Hydrogen bonds: D:S.240 Salt bridges: D:H.22 Metal complexes: D:H.22 CLA.22: 12 residues within 4Å: Chain D: H.8, H.25, V.29, W.32, F.461 Ligands: CLA.13, CLA.16, CLA.20, CLA.21, CLA.23, BCR.26, BCR.27 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:V.29, D:V.29, D:W.32, D:W.32, D:F.461, D:F.461 Salt bridges: D:H.8, D:H.8 Metal complexes: D:H.25 CLA.23: 16 residues within 4Å: Chain D: L.2, V.7, H.8, V.10, L.11, A.21, M.24, L.28, W.114 Chain J: Q.8, V.10 Chain K: F.21 Ligands: CLA.20, CLA.21, CLA.22, BCR.26 6 PLIP interactions: 1 interactions with chain K, 5 interactions with chain D, Hydrophobic interactions: K:F.21, D:V.7, D:L.11, D:M.24, D:L.28, D:W.114 CLA.24: 19 residues within 4Å: Chain D: I.19, H.22, L.23, L.121, L.132, M.137, I.140, H.141, L.144 Chain H: L.6, L.10, L.13, N.14 Ligands: CLA.13, CLA.14, CLA.19, CLA.21, CLA.25, BCR.28 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain H, Hydrophobic interactions: D:I.19, D:L.121, D:L.132, D:I.140, D:L.144, H:L.6, H:L.10, H:L.10, H:L.13 Metal complexes: D:H.141 CLA.25: 12 residues within 4Å: Chain D: I.19, L.23, L.106, A.109, W.112, H.113, L.119 Chain H: T.4, L.6, G.7 Ligands: CLA.24, BCR.28 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain H, Hydrophobic interactions: D:I.19, D:I.19, D:L.23, D:L.106, D:A.109, D:W.112, D:W.112, D:L.119, H:L.6 pi-Stacking: D:W.112 Metal complexes: D:H.113 CLA.33: 18 residues within 4Å: Chain C: V.157, M.172, I.176, F.180, F.182, M.183 Chain E: H.187, M.188, V.191, A.192, L.195, G.196 Chain J: L.30 Ligands: CLA.2, PHO.4, MGE.31, CLA.36, PQ9.38 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E, Hydrophobic interactions: C:V.157, C:I.176, C:F.180, C:F.182, E:V.191 Hydrogen bonds: E:H.187 CLA.36: 26 residues within 4Å: Chain C: M.183, F.206 Chain E: L.112, P.139, V.142, S.145, V.146, F.171, L.172, F.175, Q.176, W.181, T.182, H.187, G.190, V.191, V.194, L.195, L.269, S.272, A.273, V.276 Ligands: CLA.2, CLA.3, PHO.5, CLA.33 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain C, Hydrophobic interactions: E:L.112, E:P.139, E:V.142, E:F.171, E:L.172, E:L.172, E:F.175, E:Q.176, E:T.182, E:V.191, E:V.191, E:V.194, E:V.194, E:L.195, C:F.206 pi-Stacking: E:W.181 CLA.37: 22 residues within 4Å: Chain E: C.30, L.33, L.79, L.80, L.81, L.82, W.83, W.94, G.99, T.102, F.103, L.106, H.107 Chain H: L.38, L.42 Chain M: G.12, L.13, V.19, L.20 Ligands: CLA.17, BCR.39, UNL.50 13 PLIP interactions: 9 interactions with chain E, 3 interactions with chain M, 1 interactions with chain H, Hydrophobic interactions: E:L.81, E:L.82, E:W.83, E:W.83, E:W.83, E:F.103, E:L.106, M:L.13, M:V.19, M:L.20, H:L.38 Hydrogen bonds: E:L.82 pi-Stacking: E:F.103

2 x PHO: PHEOPHYTIN A(Non-covalent)(Covalent)

PHO.4: 26 residues within 4Å: Chain C: 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, I.176, T.179, R.279, V.283 Chain E: L.195, A.198, L.199, A.202, I.203, W.243, F.247 Ligands: CLA.2, CLA.33 21 PLIP interactions: 4 interactions with chain E, 17 interactions with chain C Hydrophobic interactions: E:L.195, E:A.198, E:A.202, E:I.203, C:L.41, C:A.44, C:F.48, C:F.48, C:I.115, C:F.119, C:F.119, C:Y.126, C:A.146, C:L.174, C:L.174, C:I.176, C:T.179, C:R.279 Hydrogen bonds: C:Y.126, C:Q.130, C:Y.147 PHO.5: 29 residues within 4Å: Chain C: F.206, A.209, L.210, A.213, M.214 Chain E: L.27, A.31, A.34, L.35, W.38, I.104, G.108, G.111, L.112, F.115, Q.119, N.132, A.135, F.136, P.139, F.143, F.163, G.164, V.165, I.168, P.265, L.269 Ligands: CLA.3, CLA.36 22 PLIP interactions: 20 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:A.31, E:A.34, E:L.35, E:W.38, E:W.38, E:W.38, E:W.38, E:I.104, E:L.112, E:F.115, E:A.135, E:F.136, E:P.139, E:F.143, E:V.165, E:I.168, E:P.265, E:L.269, C:F.206, C:A.213 Hydrogen bonds: E:N.132 pi-Stacking: E:F.136

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

BCR.7: 17 residues within 4Å: Chain C: V.35, I.38, L.42, A.43, I.46, C.47, I.50, A.51, A.54, A.55, P.56, I.96, L.102, W.105, L.106 Chain I: F.15 Ligands: CLA.6 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.35, C:I.38, C:A.43, C:I.46, C:I.46, C:I.50, C:A.51, C:I.96, C:L.102, C:W.105, C:L.106, C:L.106 BCR.26: 16 residues within 4Å: Chain D: M.24, L.28, F.107, A.110, C.111, W.114 Chain K: L.6, I.9, A.10, L.13 Ligands: CLA.16, CLA.22, CLA.23, BCR.27, MGE.29, LMT.32 9 PLIP interactions: 4 interactions with chain K, 5 interactions with chain D Hydrophobic interactions: K:L.6, K:I.9, K:A.10, K:L.13, D:L.28, D:L.28, D:F.107, D:W.114, D:W.114 BCR.27: 13 residues within 4Å: Chain D: L.28, G.31, W.32, S.35, I.100, V.101, S.103, G.104 Ligands: CLA.13, CLA.16, CLA.22, BCR.26, MGE.29 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.28, D:W.32, D:V.101 BCR.28: 14 residues within 4Å: Chain D: W.90, L.102, L.105, L.106, L.108, A.109, C.111, W.112, V.115, Y.116 Ligands: CLA.14, CLA.15, CLA.24, CLA.25 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.90, D:L.102, D:L.106, D:V.115, D:Y.116 BCR.39: 14 residues within 4Å: Chain E: Y.32, L.33, G.36, G.37, L.39, T.40, L.100, F.103 Chain G: P.29, T.30, F.33, I.37 Ligands: CLA.37, MGE.40 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: E:Y.32, E:L.39, E:L.39, E:L.39, E:T.40, E:L.100, E:F.103, E:F.103, G:P.29, G:F.33, G:I.37 BCR.46: 14 residues within 4Å: Chain H: F.33, M.34, L.36, F.37, V.39, F.40, I.43 Chain M: I.2, L.6, F.10 Ligands: CLA.10, CLA.11, CLA.12, CLA.18 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain M Hydrophobic interactions: H:F.33, H:F.37, H:F.37, H:F.37, H:F.37, H:V.39, M:I.2, M:L.6

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

CL.8: 4 residues within 4Å: Chain C: N.181, H.332 Chain E: K.307, L.311 Ligand excluded by PLIP

7 x MGE: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE(Non-covalent)(Covalent)

MGE.9: 8 residues within 4Å: Chain C: W.97, F.117, L.120, S.124, F.155 Chain I: K.5, Y.9 Ligands: CLA.6 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain I Hydrophobic interactions: C:F.117, C:L.120, C:F.155, C:F.155 Hydrogen bonds: C:W.97, I:Y.9 MGE.29: 16 residues within 4Å: Chain D: T.326, G.327, K.331, W.449, F.452, V.456 Chain J: F.35 Chain K: L.6, A.10, L.13, F.14, V.17 Ligands: CLA.16, BCR.26, BCR.27, LMT.32 13 PLIP interactions: 7 interactions with chain D, 4 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: D:W.449, D:F.452, D:F.452, K:L.13, K:F.14, K:V.17, J:F.35, J:F.35 Hydrogen bonds: D:Y.39, D:T.326, D:T.326, D:K.331, K:N.4 MGE.31: 24 residues within 4Å: Chain B: R.10 Chain D: P.3, W.4, Y.5 Chain E: W.256, F.259, F.260, F.263 Chain J: E.11, L.12, N.13, S.16, L.19, G.20, L.22, L.23, V.26 Chain K: P.18, F.21, L.22 Ligands: CLA.33, PQ9.38, MGE.41, MGE.42 13 PLIP interactions: 7 interactions with chain J, 4 interactions with chain E, 2 interactions with chain K Hydrophobic interactions: J:L.19, J:L.22, J:L.22, J:V.26, E:F.259, E:F.260, E:F.263, E:F.263, K:F.21, K:L.22 Hydrogen bonds: J:E.11, J:N.13, J:S.16 MGE.40: 10 residues within 4Å: Chain E: Y.57, G.60, C.61, N.62, F.63 Chain G: T.30, I.37, M.40, Q.41 Ligands: BCR.39 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain E Hydrogen bonds: G:M.40, G:Q.41, E:F.63 Hydrophobic interactions: E:F.63, E:F.63 MGE.41: 16 residues within 4Å: Chain B: R.10 Chain D: W.4, Y.5, R.6, F.463, W.467, F.478 Chain E: Y.131, R.255, F.259, F.263, V.266, T.267 Ligands: CLA.16, CLA.20, MGE.31 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:W.4, D:Y.5, D:F.463, D:F.463, E:F.259, E:F.263, E:F.263, E:V.266 Hydrogen bonds: D:Y.5, D:R.6, E:Y.131, E:R.255 MGE.42: 20 residues within 4Å: Chain E: F.247, I.249, A.250, F.251, S.252, N.253, W.256 Chain J: T.15, Y.18, L.19, L.22, V.26, L.29 Chain L: F.10, I.13, F.17, A.20, I.21 Ligands: MGE.31, PQ9.38 10 PLIP interactions: 3 interactions with chain J, 5 interactions with chain L, 2 interactions with chain E Hydrophobic interactions: J:L.19, J:V.26, J:L.29, L:F.10, L:I.13, L:F.17, L:F.17, L:A.20, E:F.251 Hydrogen bonds: E:S.252 MGE.48: 7 residues within 4Å: Chain K: L.16, I.23, E.30, S.31, Q.33 Chain L: F.19 Ligands: SQD.47 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:L.16, K:I.23, L:F.19 Hydrogen bonds: K:S.31

2 x UNL: UNKNOWN LIGAND

UNL.30: 9 residues within 4Å: Chain D: A.227, L.228, R.229 Chain E: D.9, K.13, W.22 Chain M: F.24 Ligands: CLA.17, UNL.50 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain M, 2 interactions with chain D Hydrophobic interactions: E:W.22, M:F.24, D:L.228 Salt bridges: E:K.13 Hydrogen bonds: D:R.229 UNL.50: 9 residues within 4Å: Chain E: W.22, S.23, L.117, F.120, E.121 Chain H: L.38 Chain M: L.20 Ligands: UNL.30, CLA.37 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain H, 1 interactions with chain M Hydrophobic interactions: E:L.117, E:E.121, H:L.38, M:L.20

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

LMT.32: 4 residues within 4Å: Chain D: Y.39 Chain K: L.6 Ligands: BCR.26, MGE.29 No protein-ligand interaction detected (PLIP) LMT.34: 4 residues within 4Å: Chain C: L.72, Y.73 Chain E: R.294 Ligands: LMT.49 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:R.294, E:R.294, C:L.72, C:Y.73 LMT.49: 6 residues within 4Å: Chain C: V.49, I.53, L.72 Chain L: M.1, I.4 Ligands: LMT.34 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: L:I.4, C:V.49 Hydrogen bonds: L:M.1, L:M.1

1 x FE2: FE (II) ION(Non-covalent)

FE2.35: 5 residues within 4Å: Chain C: H.215, H.272 Chain E: H.204, E.231, H.258 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Metal complexes: E:H.204, E:E.231, E:H.258, C:H.215

1 x PQ9: 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE(Non-covalent)

PQ9.38: 23 residues within 4Å: Chain E: M.189, A.192, L.199, L.200, I.203, H.204, T.207, Y.234, M.236, A.239, N.240, W.243, F.247, A.250, F.251, L.257, F.260, V.264 Chain J: L.29, L.30 Ligands: MGE.31, CLA.33, MGE.42 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain J Hydrophobic interactions: E:M.189, E:L.199, E:L.200, E:Y.234, E:W.243, E:F.247, E:F.251, E:L.257, E:F.260, E:V.264, J:L.29, J:L.30, J:L.30 Hydrogen bonds: E:F.251

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

HTG.43: 4 residues within 4Å: Chain E: W.4, F.5 Chain H: W.24, P.28 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.4, E:F.5

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

DGD.44: 24 residues within 4Å: Chain D: Y.192, F.249, Y.257, Y.272, Q.273, S.276, Y.278, F.462 Chain E: G.76, H.77, L.79, A.109, I.113, V.144, L.152, S.155 Chain H: L.45, Y.48, N.49, V.59, S.60, W.61 Ligands: CLA.11, CLA.17 12 PLIP interactions: 6 interactions with chain E, 4 interactions with chain D, 2 interactions with chain H Hydrophobic interactions: E:L.79, E:A.109, E:I.113, D:F.462 Hydrogen bonds: E:H.77, E:H.77, E:S.155, D:Y.192, D:Y.192, D:S.276, H:V.59, H:S.60

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

HEM.45: 9 residues within 4Å: Chain F: H.23, I.25, T.26, I.27, L.30 Chain G: R.19, V.23, H.24, V.28 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain G, Hydrophobic interactions: F:H.23, F:I.25, F:I.27, G:V.23 Salt bridges: G:R.19 pi-Stacking: G:H.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, Y. et al., Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063. Nat.Plants (2021)

Release Date

2021-06-30

Peptides

Photosystem II reaction center Psb28 protein: A
Tsl0063 protein: B
Photosystem II protein D1: C
Photosystem II CP47 reaction center protein: D
Photosystem II D2 protein: E
Cytochrome b559 subunit alpha: F
Cytochrome b559 subunit beta: G
Photosystem II reaction center protein H: H
Photosystem II reaction center protein I: 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 protein X: M
unidentified transmembrane protein: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
a

D
b

E
d

F
e

G
f

H
h

I
i

J
l

K
m

L
t

M
x

N
C

Membrane

We predict this structure to be a membrane protein.
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Photosystem II reaction center Psb28 protein

Tsl0063 protein

Photosystem II protein D1

Photosystem II CP47 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 L

Photosystem II reaction center protein M

Photosystem II reaction center protein T

Photosystem II reaction center protein X

unidentified transmembrane protein

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