SMTL ID : 3t6d.1

Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC 19567) substrain-08

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 20 residues within 4Å: Chain A: Y.76, K.77, N.78, V.79, K.80, V.81, L.82, F.90, M.94, M.97, T.98, S.102, C.107, C.110, H.111, L.116, A.117, Y.124, A.127, R.128 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.76, A:F.90, A:F.90, A:M.94, A:L.116, A:L.116, A:A.127, A:R.128 Hydrogen bonds: A:K.77, A:N.78, A:N.78, A:K.80, A:V.81, A:L.82 Salt bridges: A:R.128 pi-Stacking: A:F.90, A:Y.124 Metal complexes: A:H.111 HEC.2: 24 residues within 4Å: Chain A: M.97, V.101, Y.109, Y.122, P.123, V.126, M.130, L.131, M.133, T.134, T.151, C.152, C.155, H.156, P.160, L.161, P.162, M.297, L.302, L.309, R.313, P.321, T.327 Ligands: HEC.4 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:V.101, A:P.123, A:V.126, A:M.130, A:L.131, A:L.161, A:L.302, A:P.321, A:T.327 Salt bridges: A:R.313, A:R.313 Metal complexes: A:H.156 HEC.3: 23 residues within 4Å: Chain A: V.221, R.222, V.223, V.224, T.249, M.253, M.254, S.257, T.262, N.263, C.264, C.267, H.268, F.273, E.274, R.284, A.287, W.288, I.291, R.292 Chain C: Y.162 Chain D: I.189 Ligands: HEC.4 27 PLIP interactions: 25 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: A:V.221, A:T.249, A:M.253, A:T.262, A:F.273, A:F.273, A:F.273, A:F.273, A:R.284, A:A.287, A:W.288, A:I.291, D:I.189, C:Y.162 Hydrogen bonds: A:V.223, A:V.224, A:Q.226, A:E.274 Water bridges: A:V.221, A:R.222, A:R.284, A:R.292, A:R.292 Salt bridges: A:R.222, A:R.292 pi-Cation interactions: A:R.284 Metal complexes: A:H.268 HEC.4: 27 residues within 4Å: Chain A: I.137, H.144, V.145, A.146, T.148, G.149, V.150, I.256, L.260, F.266, Q.283, I.286, A.287, G.290, I.291, M.293, V.294, D.324, C.325, C.328, H.329, T.333, K.334, P.335 Ligands: HEC.2, HEC.3, GOL.31 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.137, A:V.145, A:V.150, A:I.256, A:L.260, A:I.286, A:A.287, A:I.291, A:V.294, A:K.334, A:P.335 Hydrogen bonds: A:T.148, A:T.148, A:Q.283 Water bridges: A:K.334 Salt bridges: A:K.334, A:K.334 Metal complexes: A:H.144, A:H.329

24 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.5: 10 residues within 4Å: Chain A: R.236 Chain B: H.3 Chain D: L.165, L.283, T.287, F.288 Ligands: SO4.17, GOL.35, GOL.76, LDA.130 Ligand excluded by PLIP LDA.6: 3 residues within 4Å: Chain A: F.22 Chain C: F.246, F.254 Ligand excluded by PLIP LDA.50: 9 residues within 4Å: Chain B: L.29, R.33 Chain D: F.202, G.205, F.206, F.256 Ligands: BCB.89, LDA.93, HTO.140 Ligand excluded by PLIP LDA.51: 5 residues within 4Å: Chain B: A.5, L.6, A.7, L.15 Ligands: HTO.70 Ligand excluded by PLIP LDA.52: 5 residues within 4Å: Chain B: Q.14, L.15, Y.18, A.19 Ligands: LDA.53 Ligand excluded by PLIP LDA.53: 3 residues within 4Å: Chain B: Y.18 Ligands: LDA.52, LDA.95 Ligand excluded by PLIP LDA.54: 12 residues within 4Å: Chain B: R.34, Y.41, P.42, V.59, Y.60, L.62, P.63, Y.64, P.79, R.80, R.81 Ligands: HTO.69 Ligand excluded by PLIP LDA.93: 8 residues within 4Å: Chain B: W.25 Chain C: Y.29 Chain D: I.254, G.255, F.256 Ligands: LDA.50, LDA.94, MQ9.118 Ligand excluded by PLIP LDA.94: 4 residues within 4Å: Chain C: Y.29 Ligands: BCB.89, LDA.93, MQ9.118 Ligand excluded by PLIP LDA.95: 16 residues within 4Å: Chain B: W.17 Chain C: D.60, F.62 Chain D: Y.195, Y.196, C.197, P.198, G.201, W.295, C.296, H.299, G.300, A.301 Ligands: LDA.53, BCB.89, GOL.115 Ligand excluded by PLIP LDA.96: 5 residues within 4Å: Chain C: W.59, P.61, I.64, Y.148, I.150 Ligand excluded by PLIP LDA.97: 9 residues within 4Å: Chain C: L.75, G.76, A.77, Q.87, T.90, V.91, W.142 Ligands: LDA.98, HTO.105 Ligand excluded by PLIP LDA.98: 7 residues within 4Å: Chain C: L.75, G.76, A.77, L.137 Ligands: LDA.97, LDA.101, GOL.113 Ligand excluded by PLIP LDA.99: 5 residues within 4Å: Chain C: L.75, L.137, G.140 Ligands: GOL.113, GOL.116 Ligand excluded by PLIP LDA.100: 4 residues within 4Å: Chain C: R.231, F.235, N.239, L.242 Ligand excluded by PLIP LDA.101: 5 residues within 4Å: Chain C: L.94, C.122, I.125, C.129 Ligands: LDA.98 Ligand excluded by PLIP LDA.123: 5 residues within 4Å: Chain D: F.33, Y.34, S.35, Y.36, W.37 Ligand excluded by PLIP LDA.124: 7 residues within 4Å: Chain D: W.23, S.54, L.122, G.125, S.126, S.133 Ligands: SO4.132 Ligand excluded by PLIP LDA.125: 4 residues within 4Å: Chain D: W.146, A.150, F.153 Ligands: SO4.134 Ligand excluded by PLIP LDA.126: 14 residues within 4Å: Chain B: V.27, Y.31 Chain C: N.199, P.200, G.201 Chain D: G.141, T.142, H.143, W.146, R.265, W.268, F.269 Ligands: SO4.131, SO4.134 Ligand excluded by PLIP LDA.127: 7 residues within 4Å: Chain D: L.67, I.68, F.71, N.72, A.75, W.112 Ligands: GOL.148 Ligand excluded by PLIP LDA.128: 7 residues within 4Å: Chain D: I.104, P.105, P.106, L.107, H.108, G.111 Ligands: GOL.148 Ligand excluded by PLIP LDA.129: 10 residues within 4Å: Chain A: G.237, K.238 Chain D: Y.100, G.101, M.102, G.103, A.164, L.165, G.167 Ligands: GOL.35 Ligand excluded by PLIP LDA.130: 4 residues within 4Å: Chain B: I.12, V.16 Ligands: LDA.5, GOL.76 Ligand excluded by PLIP

1 x DGA: DIACYL GLYCEROL(Covalent)

DGA.7: 12 residues within 4Å: Chain A: C.21, F.22 Chain C: P.171, G.172, M.174, S.178, T.243, F.246, W.262, W.265 Ligands: UQ9.92, BCB.119 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:M.174, C:T.243, C:F.246, C:W.265

41 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain A: R.54, Q.57, R.177 Ligands: HTO.28 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: T.227, A.228 Chain D: L.294, K.298 Ligands: GOL.141 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: T.181, H.182 Ligands: GOL.39 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: V.81, E.132, R.135 Ligands: SO4.25, GOL.43 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain A: R.313 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: T.211, N.216, K.218, R.219 Ligands: GOL.36 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain A: S.340, R.341, L.342, Q.343, D.344 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: V.65, K.66 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: P.63, A.64 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: G.233, E.239 Ligands: LDA.5 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Ligands: SO4.23 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: L.62, E.99 Ligands: GOL.47 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain A: P.45, V.48, K.49, K.52 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: D.296, M.299, N.300 Ligands: SO4.24 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain A: C.21, F.22, E.23 Chain C: W.255, R.257 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: E.113, N.114 Ligands: SO4.18 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: W.141, D.296 Ligands: SO4.21, GOL.37 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain A: R.135, A.136, T.139, N.140, I.351 Ligands: SO4.11, GOL.43 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain B: Y.117, E.119, E.122, R.233, K.237 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain B: K.131, R.175 Ligand excluded by PLIP SO4.57: 6 residues within 4Å: Chain B: R.33, R.37, Y.41, L.43, E.61 Chain D: R.251 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain B: L.30, R.34 Ligands: HTO.69 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain B: R.153, G.154, L.155 Ligand excluded by PLIP SO4.60: 6 residues within 4Å: Chain B: D.202, K.204 Chain D: Y.7, Q.9 Ligands: SO4.67, GOL.82 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain B: A.160, D.161, G.162 Ligand excluded by PLIP SO4.62: 5 residues within 4Å: Chain B: V.124, A.126, G.130, K.131, A.132 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain B: L.22, W.25, T.26, L.30 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain B: N.106, P.107, Q.217, Y.248 Ligand excluded by PLIP SO4.65: 4 residues within 4Å: Chain B: L.224, Q.225, S.226, R.227 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain B: H.9 Chain D: K.298 Ligands: GOL.141 Ligand excluded by PLIP SO4.67: 5 residues within 4Å: Chain B: D.202, K.204 Chain D: Y.3 Ligands: SO4.60, GOL.82 Ligand excluded by PLIP SO4.102: 5 residues within 4Å: Chain C: V.26, G.27, P.28, Y.29 Ligands: MQ9.118 Ligand excluded by PLIP SO4.103: 6 residues within 4Å: Chain B: L.70, P.71, H.72, G.73 Chain C: K.205 Ligands: GOL.81 Ligand excluded by PLIP SO4.131: 5 residues within 4Å: Chain C: N.199 Chain D: H.143, R.265 Ligands: GOL.72, LDA.126 Ligand excluded by PLIP SO4.132: 6 residues within 4Å: Chain D: W.23, Y.50, G.52, A.53, S.54 Ligands: LDA.124 Ligand excluded by PLIP SO4.133: 5 residues within 4Å: Chain B: T.211, L.246 Chain D: A.1, R.226 Ligands: HTO.104 Ligand excluded by PLIP SO4.134: 5 residues within 4Å: Chain D: Y.132, T.142, W.146 Ligands: LDA.125, LDA.126 Ligand excluded by PLIP SO4.135: 2 residues within 4Å: Chain D: Y.308, L.309 Ligand excluded by PLIP SO4.136: 4 residues within 4Å: Chain D: A.307, Y.308, L.309, P.310 Ligand excluded by PLIP SO4.137: 3 residues within 4Å: Chain D: Y.100, I.104, P.106 Ligand excluded by PLIP SO4.138: 2 residues within 4Å: Chain D: Y.132, R.136 Ligand excluded by PLIP

13 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.26: 7 residues within 4Å: Chain A: N.84, R.135, P.346, E.347, P.350, I.351, K.352 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.352 Hydrogen bonds: A:N.84, A:R.135, A:R.135 HTO.27: 6 residues within 4Å: Chain A: A.64, V.65, R.92, Q.343, D.344, P.346 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.65, A:D.344 Water bridges: A:E.89, A:E.89, A:D.344 HTO.28: 8 residues within 4Å: Chain A: T.47, A.50, K.51, R.54, Y.164, N.175 Ligands: SO4.8, GOL.114 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.47, A:A.50, A:K.51 Hydrogen bonds: A:R.54, A:N.175 Water bridges: A:Q.330 HTO.29: 5 residues within 4Å: Chain A: P.24, P.25, H.44, A.46 Ligands: GOL.45 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.24 Hydrogen bonds: A:H.44 Water bridges: A:A.46 HTO.68: 5 residues within 4Å: Chain B: Q.225, S.226, R.227, D.228, Q.229 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.228, B:Q.229 Hydrogen bonds: B:R.227 HTO.69: 6 residues within 4Å: Chain B: T.26, L.30, Y.31, R.34 Ligands: LDA.54, SO4.58 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.26 Hydrogen bonds: B:R.34 Water bridges: B:L.30 HTO.70: 6 residues within 4Å: Chain B: A.5, L.6, A.7 Ligands: LDA.51, GOL.76, GOL.84 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.7 HTO.104: 5 residues within 4Å: Chain C: G.114, W.115, H.116 Chain D: A.1 Ligands: SO4.133 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.115 Water bridges: C:I.113 HTO.105: 8 residues within 4Å: Chain C: A.77, A.78, L.80, G.84, Q.87, A.88 Ligands: LDA.97, HTO.106 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.87 Hydrogen bonds: C:A.78 HTO.106: 4 residues within 4Å: Chain C: A.77, P.79, L.80 Ligands: HTO.105 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.80 Water bridges: C:L.81 HTO.107: 2 residues within 4Å: Chain C: F.33, V.36 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.33, C:V.36 HTO.108: 2 residues within 4Å: Chain C: K.72, Y.73 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.73 Water bridges: C:K.72 HTO.140: 8 residues within 4Å: Chain B: W.17, W.21 Chain C: I.150 Chain D: P.198, G.201, F.202 Ligands: LDA.50, BCB.89 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:P.198, D:G.201 Hydrophobic interactions: C:I.150

54 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 8 residues within 4Å: Chain A: V.42, D.258, T.262, N.263 Chain C: L.165, T.256, R.257, G.258 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain A: T.32, E.41, F.266, Q.283, K.334 Ligands: HEC.4, GOL.44 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain A: E.187, T.188, R.189, S.190 Chain D: H.78, D.80 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain A: E.41, K.51, L.260, G.261, G.331, V.332, T.333 Ligands: GOL.38 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain A: T.275, W.276, G.277 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain A: R.236, G.237, K.238, E.239 Ligands: LDA.5, LDA.129 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain A: L.168, Q.317 Ligands: SO4.13 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain A: N.140, W.141, Q.143, W.289 Ligands: SO4.24, GOL.145 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain A: T.30, E.41, L.43 Ligands: GOL.33, GOL.44 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain A: P.180, T.181, H.182, R.185 Ligands: SO4.10 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain A: Y.207, M.212, S.244, D.245 Chain D: K.97 Ligand excluded by PLIP GOL.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain A: T.181, E.184, K.198 Chain C: D.268, S.273 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain A: R.129, A.136, Y.301 Ligands: SO4.11, SO4.25 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain A: K.334 Ligands: GOL.31, GOL.38 Ligand excluded by PLIP GOL.45: 3 residues within 4Å: Chain A: P.24, P.25 Ligands: HTO.29 Ligand excluded by PLIP GOL.46: 2 residues within 4Å: Chain A: P.180, R.185 Ligand excluded by PLIP GOL.47: 3 residues within 4Å: Chain A: L.62, P.63 Ligands: SO4.19 Ligand excluded by PLIP GOL.48: 3 residues within 4Å: Chain A: P.310, A.311, S.312 Ligand excluded by PLIP GOL.49: 1 residues within 4Å: Chain A: N.114 Ligand excluded by PLIP GOL.71: 5 residues within 4Å: Chain B: L.137, A.140, T.141, F.143, R.153 Ligand excluded by PLIP GOL.72: 7 residues within 4Å: Chain B: Y.31, E.35, R.38, K.66 Chain C: N.199 Chain D: R.265 Ligands: SO4.131 Ligand excluded by PLIP GOL.73: 3 residues within 4Å: Chain B: V.124, D.125, A.126 Ligand excluded by PLIP GOL.74: 2 residues within 4Å: Chain B: T.250, R.253 Ligand excluded by PLIP GOL.75: 4 residues within 4Å: Chain B: D.149, V.150, D.151, K.205 Ligand excluded by PLIP GOL.76: 7 residues within 4Å: Chain B: H.3, G.4, A.5 Chain D: F.288 Ligands: LDA.5, HTO.70, LDA.130 Ligand excluded by PLIP GOL.77: 2 residues within 4Å: Chain B: E.147 Chain D: Y.36 Ligand excluded by PLIP GOL.78: 2 residues within 4Å: Chain B: R.80, R.82 Ligand excluded by PLIP GOL.79: 4 residues within 4Å: Chain B: N.220, V.221, P.222, R.223 Ligand excluded by PLIP GOL.80: 5 residues within 4Å: Chain B: L.90, A.91, Q.92 Chain C: R.7 Ligands: GOL.85 Ligand excluded by PLIP GOL.81: 4 residues within 4Å: Chain B: P.71, H.72 Chain C: K.205 Ligands: SO4.103 Ligand excluded by PLIP GOL.82: 4 residues within 4Å: Chain B: K.204, K.205 Ligands: SO4.60, SO4.67 Ligand excluded by PLIP GOL.83: 3 residues within 4Å: Chain B: K.204, K.207, V.209 Ligand excluded by PLIP GOL.84: 4 residues within 4Å: Chain B: A.7, Q.8, H.9 Ligands: HTO.70 Ligand excluded by PLIP GOL.85: 6 residues within 4Å: Chain B: E.87, L.88, K.89, L.90, T.104 Ligands: GOL.80 Ligand excluded by PLIP GOL.86: 6 residues within 4Å: Chain B: E.97, G.98, A.99 Chain C: L.2, R.7, R.10 Ligand excluded by PLIP GOL.87: 2 residues within 4Å: Chain B: T.141, D.142 Ligand excluded by PLIP GOL.109: 9 residues within 4Å: Chain B: E.177, Y.179 Chain C: I.224, G.225, A.226, L.227, S.228 Chain D: G.42, D.43 Ligand excluded by PLIP GOL.110: 7 residues within 4Å: Chain A: R.35 Chain C: A.52, Q.55, G.56, S.65, L.81 Ligands: GOL.142 Ligand excluded by PLIP GOL.111: 4 residues within 4Å: Chain C: D.204, K.205, K.207 Chain D: G.139 Ligand excluded by PLIP GOL.112: 5 residues within 4Å: Chain C: P.57, T.58, W.59, D.60 Ligands: GOL.115 Ligand excluded by PLIP GOL.113: 8 residues within 4Å: Chain C: K.72, Y.73, G.74, L.75, G.76 Ligands: LDA.98, LDA.99, GOL.116 Ligand excluded by PLIP GOL.114: 2 residues within 4Å: Chain C: R.257 Ligands: HTO.28 Ligand excluded by PLIP GOL.115: 5 residues within 4Å: Chain C: W.59, D.60, P.61 Ligands: LDA.95, GOL.112 Ligand excluded by PLIP GOL.116: 7 residues within 4Å: Chain C: L.71, K.72, G.74, G.140, S.141 Ligands: LDA.99, GOL.113 Ligand excluded by PLIP GOL.141: 7 residues within 4Å: Chain A: T.227, A.228, L.229 Chain B: Y.2 Chain D: K.298 Ligands: SO4.9, SO4.66 Ligand excluded by PLIP GOL.142: 6 residues within 4Å: Chain A: F.34 Chain C: S.65 Chain D: D.304, Y.305, P.306 Ligands: GOL.110 Ligand excluded by PLIP GOL.143: 5 residues within 4Å: Chain D: W.23, G.24, D.25, N.26, D.27 Ligand excluded by PLIP GOL.144: 4 residues within 4Å: Chain D: D.27, G.52, A.53, I.56 Ligand excluded by PLIP GOL.145: 6 residues within 4Å: Chain A: Q.143, W.289 Chain D: P.319, G.320, A.321 Ligands: GOL.37 Ligand excluded by PLIP GOL.146: 4 residues within 4Å: Chain D: D.25, N.26, D.27, R.28 Ligand excluded by PLIP GOL.147: 3 residues within 4Å: Chain D: P.15, H.16, Y.34 Ligand excluded by PLIP GOL.148: 4 residues within 4Å: Chain D: L.107, W.112 Ligands: LDA.127, LDA.128 Ligand excluded by PLIP GOL.149: 3 residues within 4Å: Chain D: G.30, K.31 Ligands: BCB.119 Ligand excluded by PLIP

4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)

BCB.88: 32 residues within 4Å: Chain C: F.97, P.124, I.125, M.127, F.128, L.131, V.157, N.158, F.160, G.161, Y.162, W.167, H.168, G.172, H.173, S.176, V.177, L.180, F.181, I.240, F.241, G.244, G.247, T.248 Chain D: L.184, Y.195, Y.208 Ligands: BCB.89, BPB.90, MQ9.118, BCB.119, BCB.120 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:F.97, C:F.97, C:P.124, C:L.131, C:F.160, C:Y.162, C:W.167, C:W.167, C:V.177, C:L.180, C:F.181, C:I.240, C:F.241, C:F.241 Hydrogen bonds: C:S.176, C:T.248 pi-Stacking: C:W.167 Metal complexes: C:H.173 BCB.89: 23 residues within 4Å: Chain C: I.49, F.128, F.146, I.150, L.151, H.153, L.154, V.157 Chain D: Y.195, G.201, I.204, G.205, Y.208, G.209, L.212 Ligands: LDA.50, BCB.88, BPB.90, LDA.94, LDA.95, MQ9.118, BCB.120, HTO.140 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain C, Hydrophobic interactions: D:Y.195, D:I.204, D:I.204, C:I.49, C:F.128, C:F.146, C:L.154, C:V.157 pi-Stacking: D:Y.208 Metal complexes: C:H.153 BCB.119: 27 residues within 4Å: Chain C: H.168, M.174, V.177, S.178, F.181, V.182, M.185, V.220, G.221, Y.222 Chain D: M.120, F.154, V.155, I.158, V.173, I.177, W.178, H.180, I.181, L.184 Ligands: DGA.7, BCB.88, UQ9.91, BCB.120, BPB.121, NS5.122, GOL.149 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain C, Hydrophobic interactions: D:F.154, D:I.158, D:V.173, D:I.177, D:I.181, D:L.184, C:V.177, C:F.181, C:V.182, C:Y.222 Metal complexes: D:H.180 pi-Stacking: C:F.181 BCB.120: 33 residues within 4Å: Chain C: V.157, Y.162, F.181 Chain D: G.62, I.66, I.69, M.120, L.124, F.148, A.151, F.154, V.155, I.158, W.183, L.184, T.185, F.187, S.188, F.194, Y.195, H.200, S.203, I.204, A.207, Y.208, V.274, M.275, A.278, I.282 Ligands: BCB.88, BCB.89, BCB.119, BPB.121 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:I.66, D:I.69, D:L.124, D:F.148, D:A.151, D:F.154, D:F.154, D:V.155, D:W.183, D:L.184, D:F.187, D:F.194, D:Y.195, D:Y.195, D:I.204, D:A.207, D:Y.208 Hydrogen bonds: D:Y.195, D:S.203 Salt bridges: D:H.200 Metal complexes: D:H.200

2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)

BPB.90: 28 residues within 4Å: Chain C: F.41, I.42, G.45, I.49, A.93, A.96, F.97, W.100, E.104, V.117, A.120, F.121, P.124, F.128, Y.148, G.149, I.150, H.153, A.237, F.241 Chain D: Y.208, G.211, L.212, W.250, I.254 Ligands: BCB.88, BCB.89, MQ9.118 13 PLIP interactions: 1 interactions with chain D, 12 interactions with chain C Hydrophobic interactions: D:Y.208, C:I.42, C:I.49, C:A.96, C:A.120, C:F.121, C:F.121, C:F.121, C:F.128, C:Y.148, C:Y.148, C:F.241 Hydrogen bonds: C:E.104 BPB.121: 24 residues within 4Å: Chain C: F.181, A.184, M.185, L.189, V.219, V.220 Chain D: A.58, F.59, A.63, I.66, L.67, S.123, L.124, W.127, V.131, I.144, N.147, F.148, A.151, S.271, M.275 Ligands: UQ9.91, BCB.119, BCB.120 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.59, D:F.59, D:F.59, D:A.63, D:I.66, D:L.67, D:W.127, D:N.147, D:F.148, D:F.148, C:A.184, C:M.185, C:L.189 pi-Stacking: D:F.148

2 x UQ9: Ubiquinone-9(Non-covalent)

UQ9.91: 22 residues within 4Å: Chain C: S.178, V.182, L.189, H.190, L.193, I.194, E.212, N.213, F.216, V.220, Y.222, S.223, I.224, G.225, A.226, I.229, L.232 Chain D: I.49, F.59, W.127 Ligands: BCB.119, BPB.121 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.182, C:L.189, C:L.193, C:F.216, C:F.216, C:V.220, C:Y.222, C:I.229, C:L.232, D:I.49, D:F.59, D:W.127 Hydrogen bonds: C:I.224, C:G.225 UQ9.92: 6 residues within 4Å: Chain C: W.263, W.266 Chain D: F.85, F.88, F.89 Ligands: DGA.7 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.263, C:W.266, D:F.89, D:F.89, D:F.89 pi-Stacking: C:W.266

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

FE2.117: 5 residues within 4Å: Chain C: H.190, H.230 Chain D: H.217, E.232, H.264 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.217, D:E.232, D:H.264, C:H.190, C:H.230

1 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.118: 30 residues within 4Å: Chain C: Y.29, F.30, G.35, I.39, I.42, F.43, W.100, R.103 Chain D: L.212, A.216, H.217, T.220, A.246, A.247, W.250, I.254, F.256, N.257, A.258, T.259, I.260, V.263, W.266, F.270 Ligands: BCB.88, BCB.89, BPB.90, LDA.93, LDA.94, SO4.102 21 PLIP interactions: 9 interactions with chain C, 12 interactions with chain D Hydrophobic interactions: C:Y.29, C:Y.29, C:Y.29, C:I.39, C:I.42, C:F.43, C:W.100, C:W.100, C:W.100, D:L.212, D:A.246, D:W.250, D:I.254, D:F.256, D:F.256, D:I.260, D:V.263, D:W.266, D:W.266, D:F.270 Hydrogen bonds: D:A.258

1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)

NS5.122: 25 residues within 4Å: Chain D: I.66, L.67, I.69, G.70, F.71, M.73, L.74, F.88, I.104, W.113, L.114, G.117, L.118, M.120, T.121, V.155, G.159, C.160, V.173, P.174, F.175, G.176, I.177, H.180 Ligands: BCB.119 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.67, D:I.69, D:L.74, D:F.88, D:I.104, D:W.113, D:L.114, D:L.118, D:V.173, D:V.173, D:F.175, D:F.175, D:F.175, D:I.177, D:H.180

1 x HTH: (2S,3R)-heptane-1,2,3-triol(Non-covalent)

HTH.139: 2 residues within 4Å: Chain D: Y.7, K.40 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.7, D:Y.7, D:K.40 Hydrogen bonds: D:Y.7 Water bridges: D:K.40, B:D.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roszak, A.W. et al., New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory. Biochem.J. (2012)

Release Date

2011-11-23

Peptides

Photosynthetic reaction center cytochrome c subunit: A
Photosynthetic reaction center H-subunit: B
Photosynthetic reaction center L-subunit: C
Photosynthetic reaction center M-subunit: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
L

D
M

Membrane

We predict this structure to be a membrane protein.
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Photosynthetic reaction center cytochrome c subunit

Photosynthetic reaction center H-subunit

Photosynthetic reaction center L-subunit

Photosynthetic reaction center M-subunit

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