- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.77 Å
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 10 x BCR: BETA-CAROTENE(Non-covalent)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 35 x CLA: CHLOROPHYLL A(Non-covalent)
CLA.3: 29 residues within 4Å:- Chain A: F.119, V.123, F.147, P.150, V.151, A.153, V.157, F.182, M.183, L.184, F.186, Q.187, I.192, L.193, H.198, G.201, V.202, V.205, F.206, I.283, T.286, S.287, I.290
- Chain D: L.181, L.204
- Ligands: CLA.4, CLA.6, PHO.8, CLA.62
20 PLIP interactions:19 interactions with chain A, 1 interactions with chain D,- Hydrophobic interactions: A:F.119, A:F.119, A:V.123, A:F.147, A:A.153, A:L.184, A:F.186, A:Q.187, A:I.192, A:I.192, A:L.193, A:V.202, A:V.205, A:V.205, A:F.206, A:I.290, D:L.204
- pi-Stacking: A:H.198, A:H.198
- Metal complexes: A:H.198
CLA.4: 15 residues within 4Å:- Chain A: M.199, V.202, A.203, G.207, L.210, W.278
- Chain D: F.156, V.174, I.177, F.178, F.180, L.181
- Ligands: CLA.3, CLA.62, PHO.67
9 PLIP interactions:4 interactions with chain A, 5 interactions with chain D,- Hydrophobic interactions: A:V.202, A:L.210, A:W.278, D:F.156, D:F.156, D:F.178, D:F.180, D:L.181
- pi-Stacking: A:F.206
CLA.5: 20 residues within 4Å:- Chain A: P.39, C.40, T.43, L.93, Y.94, P.95, I.96, W.97, Q.113, L.114, L.117, H.118, L.121
- Chain H: V.8, Y.9, V.12, F.15
- Ligands: BCR.1, LMG.10, LMG.12
14 PLIP interactions:4 interactions with chain H, 10 interactions with chain A,- Hydrophobic interactions: H:V.8, H:Y.9, H:F.15, A:P.39, A:T.43, A:P.95, A:W.97, A:W.97, A:L.114, A:L.117
- Hydrogen bonds: H:Y.9, A:I.96
- Salt bridges: A:H.118
- Metal complexes: A:H.118
CLA.6: 20 residues within 4Å:- Chain A: T.45, I.49, V.157, F.158, M.172, I.176, T.179, F.180, M.183
- Chain D: M.197, V.200, A.201, L.204
- Chain K: L.31
- Ligands: CLA.3, PHO.8, CLA.62, LHG.65, PL9.68, LHG.76
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain D,- Hydrophobic interactions: A:T.45, A:I.49, A:V.157, A:F.158, A:F.180, D:V.200
CLA.17: 7 residues within 4Å:- Chain B: W.185, G.186, P.187, F.190
- Chain G: F.41
- Ligands: CLA.18, BCR.73
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain G,- Hydrophobic interactions: B:P.187, B:F.190, B:F.190, G:F.41, G:F.41
CLA.18: 24 residues within 4Å:- Chain B: A.184, G.189, F.190, P.192, S.200, H.201, A.204, A.205, V.208, F.246, F.247, F.250, V.251, T.255
- Chain D: L.157, L.158
- Chain G: F.38, F.41, I.45, L.46, Y.49
- Ligands: CLA.17, CLA.19, DGD.72
15 PLIP interactions:2 interactions with chain G, 11 interactions with chain B, 2 interactions with chain D,- Hydrophobic interactions: G:F.38, G:I.45, B:F.190, B:F.190, B:F.190, B:H.201, B:V.208, B:F.246, B:F.247, B:F.247, B:F.250, D:L.157, D:L.158
- pi-Stacking: B:H.201
- Metal complexes: B:H.201
CLA.19: 26 residues within 4Å:- Chain B: R.68, L.69, S.146, L.149, C.150, F.153, I.166, I.198, H.201, H.202, A.244, F.247, A.248, V.251, V.252, S.262
- Chain G: F.38, L.42
- Ligands: CLA.18, CLA.20, CLA.21, CLA.22, CLA.23, CLA.24, CLA.25, BCR.73
15 PLIP interactions:13 interactions with chain B, 2 interactions with chain G,- Hydrophobic interactions: B:L.69, B:L.149, B:L.149, B:F.153, B:A.244, B:A.248, B:V.251, B:V.252, G:F.38, G:L.42
- Hydrogen bonds: B:R.68
- Salt bridges: B:R.68
- pi-Stacking: B:H.202
- pi-Cation interactions: B:H.201
- Metal complexes: B:H.202
CLA.20: 21 residues within 4Å:- Chain B: W.33, F.61, F.65, R.68, V.245, A.248, S.249, V.252, F.451, H.455, F.458, A.459, F.462
- Ligands: CLA.19, CLA.21, CLA.25, CLA.26, CLA.27, CLA.28, CLA.30, CLA.32
17 PLIP interactions:17 interactions with chain B,- Hydrophobic interactions: B:W.33, B:F.61, B:F.65, B:F.65, B:F.65, B:V.245, B:A.248, B:S.249, B:F.458, B:F.458, B:F.458, B:F.462, B:F.462
- Salt bridges: B:R.68
- pi-Stacking: B:H.455, B:H.455
- Metal complexes: B:H.455
CLA.21: 21 residues within 4Å:- Chain B: T.27, V.30, S.31, W.33, A.34, V.62, F.65, M.66, R.68, L.69, V.96, H.100, L.103, S.146, S.147, A.205
- Ligands: CLA.19, CLA.20, CLA.22, CLA.24, CLA.25
9 PLIP interactions:9 interactions with chain B,- Hydrophobic interactions: B:T.27, B:V.30, B:W.33, B:A.34, B:V.96, B:L.103, B:S.146
- Salt bridges: B:R.68
- Metal complexes: B:H.100
CLA.22: 21 residues within 4Å:- Chain B: L.69, G.70, V.71, W.91, V.96, T.99, H.100, L.149, G.152, F.153, F.156, H.157, F.162, G.163, P.164
- Chain T: L.11
- Ligands: BCR.16, CLA.19, CLA.21, CLA.31, LMG.35
12 PLIP interactions:11 interactions with chain B, 1 interactions with chain T,- Hydrophobic interactions: B:L.69, B:V.71, B:W.91, B:W.91, B:W.91, B:L.149, B:F.156, B:F.162, B:F.162, T:L.11
- pi-Stacking: B:H.157
- Metal complexes: B:H.157
CLA.23: 24 residues within 4Å:- Chain B: L.229, T.236, S.239, A.243, F.246, F.247, F.463, H.466, L.467, G.470, L.474
- Chain D: F.90, F.119, I.122, C.125, L.126, F.129
- Chain G: L.46
- Ligands: CLA.19, CLA.24, CLA.25, UNL.37, CLA.63, DGD.72
15 PLIP interactions:9 interactions with chain B, 5 interactions with chain D, 1 interactions with chain G,- Hydrophobic interactions: B:A.243, B:F.246, B:F.247, B:F.463, B:L.467, B:L.474, D:F.90, D:F.119, D:I.122, D:L.126, D:L.126, G:L.46
- pi-Stacking: B:H.466, B:H.466
- Metal complexes: B:H.466
CLA.24: 21 residues within 4Å:- Chain B: F.139, V.208, A.212, F.215, H.216, P.221, P.222, L.225, L.229, M.231
- Chain G: T.27, T.28, M.31, F.34, M.35
- Ligands: CLA.19, CLA.21, CLA.23, CLA.25, UNL.37, BCR.73
11 PLIP interactions:2 interactions with chain G, 9 interactions with chain B,- Hydrophobic interactions: G:M.31, G:F.34, B:F.139, B:F.139, B:V.208, B:A.212, B:F.215, B:F.215
- Salt bridges: B:H.216
- pi-Cation interactions: B:H.216
- Metal complexes: B:H.216
CLA.25: 22 residues within 4Å:- Chain B: L.19, L.135, F.139, H.142, L.143, L.145, S.146, L.229, M.231, I.234, T.236, V.237, S.240, S.241, A.244
- Ligands: CLA.19, CLA.20, CLA.21, CLA.23, CLA.24, CLA.27, CLA.30
11 PLIP interactions:11 interactions with chain B,- Hydrophobic interactions: B:L.19, B:L.135, B:F.139, B:F.139, B:L.145, B:L.229, B:M.231, B:I.234, B:T.236, B:V.237
- Hydrogen bonds: B:H.142
CLA.26: 20 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.20, CLA.27, CLA.28, CLA.29, LHG.34, LHG.76
14 PLIP interactions:14 interactions with chain B,- Hydrophobic interactions: B:W.5, B:W.5, B:H.9, B:L.238, B:I.242, B:I.242, B:F.462, B:F.462
- Hydrogen bonds: B:H.9
- Salt bridges: B:H.9, B:R.472
- pi-Stacking: B:W.468
- pi-Cation interactions: B:H.469
- Metal complexes: B:H.469
CLA.27: 20 residues within 4Å:- Chain B: H.9, V.12, L.13, L.19, V.22, H.23, H.26, T.27, I.234, V.237, L.238, S.241, I.242, V.245
- Ligands: CLA.20, CLA.25, CLA.26, CLA.28, CLA.29, CLA.30
18 PLIP interactions:18 interactions with chain B,- Hydrophobic interactions: B:V.12, B:L.13, B:L.19, B:V.22, B:H.23, B:H.26, B:T.27, B:I.234, B:I.234, B:V.237, B:L.238, B:L.238, B:V.245
- Hydrogen bonds: B:S.241
- Salt bridges: B:H.23
- pi-Stacking: B:H.26
- pi-Cation interactions: B:H.23
- Metal complexes: B:H.23
CLA.28: 13 residues within 4Å:- Chain B: H.9, H.26, V.30, W.33, F.462
- Ligands: BCR.14, BCR.15, CLA.20, CLA.26, CLA.27, CLA.29, CLA.32, LHG.34
10 PLIP interactions:10 interactions with chain B,- Hydrophobic interactions: B:V.30, B:V.30, B:W.33, B:W.33, B:F.462
- Salt bridges: B:H.9, B:H.9
- pi-Stacking: B:H.26
- pi-Cation interactions: B:H.26
- Metal complexes: B:H.26
CLA.29: 19 residues within 4Å:- Chain B: L.3, V.8, H.9, V.11, V.22, M.25, L.29, W.115
- Chain K: Q.9, V.11
- Chain L: P.86, F.89, L.93
- Ligands: BCR.14, BCR.15, CLA.26, CLA.27, CLA.28, LHG.76
8 PLIP interactions:3 interactions with chain L, 5 interactions with chain B,- Hydrophobic interactions: L:F.89, L:F.89, L:L.93, B:M.25, B:L.29, B:W.115
- pi-Stacking: B:H.9
- Metal complexes: B:H.9
CLA.30: 17 residues within 4Å:- Chain B: I.20, H.23, L.24, L.133, V.138, I.141, H.142, L.145
- Chain G: L.7, L.11, L.14, N.15
- Chain T: L.18
- Ligands: CLA.20, CLA.25, CLA.27, CLA.31
11 PLIP interactions:8 interactions with chain B, 3 interactions with chain G,- Hydrophobic interactions: B:I.20, B:L.133, B:V.138, B:I.141, B:I.141, B:L.145, G:L.7, G:L.11, G:L.14
- pi-Stacking: B:H.142
- Metal complexes: B:H.142
CLA.31: 19 residues within 4Å:- Chain B: I.20, L.24, A.110, W.113, H.114, L.120, L.122
- Chain G: T.5, L.7, G.8, L.11
- Chain T: A.15, L.18, V.19, V.21, A.22
- Ligands: BCR.16, CLA.22, CLA.30
15 PLIP interactions:10 interactions with chain B, 2 interactions with chain G, 3 interactions with chain T,- Hydrophobic interactions: B:I.20, B:L.24, B:W.113, B:W.113, B:L.120, B:L.122, G:L.7, G:L.11, T:L.18, T:L.18, T:A.22
- pi-Stacking: B:W.113, B:W.113, B:H.114
- Metal complexes: B:H.114
CLA.32: 23 residues within 4Å:- Chain B: W.33, M.37, Y.40, V.44, Q.58, G.59, F.61, L.324, F.325, R.326, A.327, G.328, W.450, F.451, F.458
- Chain D: F.195
- Chain K: F.32, F.36
- Ligands: BCR.14, BCR.15, CLA.20, CLA.28, LMG.78
17 PLIP interactions:11 interactions with chain B, 4 interactions with chain K, 1 interactions with chain D, 1 Ligand-Water interactions,- Hydrophobic interactions: B:W.33, B:Y.40, B:F.61, B:F.61, B:F.61, B:F.325, B:W.450, B:F.458, K:F.32, K:F.32, K:F.36, K:F.36, D:F.195
- Hydrogen bonds: B:G.328
- pi-Stacking: B:F.61, B:W.450
- Metal complexes: H2O.1
CLA.41: 21 residues within 4Å:- Chain C: L.82, L.155, G.158, A.159, L.162, I.211, M.217, H.224, I.227, A.265, M.269, T.272, Y.276, V.283, Y.284
- Ligands: BCR.40, CLA.42, CLA.43, CLA.46, CLA.47, CLA.51
13 PLIP interactions:13 interactions with chain C,- Hydrophobic interactions: C:L.162, C:I.211, C:I.227, C:A.265, C:M.269, C:T.272, C:Y.276, C:V.283, C:Y.284
- Hydrogen bonds: C:Y.284
- pi-Stacking: C:H.224
- pi-Cation interactions: C:H.224
- Metal complexes: C:H.224
CLA.42: 19 residues within 4Å:- Chain C: W.50, I.74, H.78, K.165, L.266, M.269, A.273, A.277, Y.284, L.413, H.417, L.420, G.421, I.424
- Ligands: CLA.41, CLA.43, CLA.44, CLA.50, LMG.59
13 PLIP interactions:13 interactions with chain C,- Hydrophobic interactions: C:W.50, C:I.74, C:K.165, C:L.266, C:M.269, C:A.273, C:L.413, C:L.420, C:I.424
- Hydrogen bonds: C:Y.284
- Salt bridges: C:H.78, C:H.417
- Metal complexes: C:H.417
CLA.43: 17 residues within 4Å:- Chain C: I.47, V.48, T.51, T.55, L.75, H.78, L.79, L.82, T.101, H.105, L.266
- Ligands: CLA.41, CLA.42, CLA.49, CLA.50, CLA.51, LMT.58
11 PLIP interactions:11 interactions with chain C,- Hydrophobic interactions: C:I.47, C:V.48, C:T.51, C:L.79, C:L.82, C:T.101, C:L.266
- Salt bridges: C:H.78
- pi-Stacking: C:H.105, C:H.105
- Metal complexes: C:H.105
CLA.44: 22 residues within 4Å:- Chain A: F.197, V.281, L.285
- Chain C: W.50, M.54, F.57, Q.71, G.72, I.74, W.412, L.413, S.416, H.417, F.423
- Chain J: P.21
- Ligands: CLA.42, CLA.48, CLA.50, DGD.54, DGD.56, LMG.59, LHG.64
11 PLIP interactions:4 interactions with chain A, 6 interactions with chain C, 1 interactions with chain J,- Hydrophobic interactions: A:F.197, A:F.197, A:V.281, A:L.285, C:I.74, C:W.412, C:W.412, C:F.423, C:F.423, J:P.21
- pi-Stacking: C:W.412
CLA.45: 24 residues within 4Å:- Chain A: F.33, L.121, A.124, M.127, G.128, W.131
- Chain C: P.204, F.251, V.252, S.260, Y.261, G.264, A.265, F.425, H.428, L.429, A.432, R.436
- Chain H: F.19, F.23
- Ligands: LMG.10, BCR.40, CLA.47, DGD.55
19 PLIP interactions:9 interactions with chain C, 8 interactions with chain A, 2 interactions with chain H,- Hydrophobic interactions: C:P.204, C:Y.261, C:Y.261, C:F.425, C:L.429, A:F.33, A:F.33, A:L.121, A:A.124, A:W.131, A:W.131, A:W.131, H:F.19, H:F.23
- Hydrogen bonds: C:Y.261
- Salt bridges: C:R.436
- pi-Stacking: C:H.428, A:W.131
- Metal complexes: C:H.428
CLA.46: 17 residues within 4Å:- Chain C: L.148, L.200, L.201, T.230, G.234, W.237, H.238, P.243, F.244, W.246, A.247, F.251, L.268
- Ligands: LMG.10, BCR.40, CLA.41, CLA.47
10 PLIP interactions:10 interactions with chain C,- Hydrophobic interactions: C:L.148, C:L.201, C:W.237, C:W.246, C:A.247, C:F.251, C:L.268
- Hydrogen bonds: C:F.244
- pi-Stacking: C:H.238
- Metal complexes: C:H.238
CLA.47: 19 residues within 4Å:- Chain C: M.144, T.145, L.148, H.151, L.155, W.246, F.251, W.253, Y.258, Y.261, S.262, A.265, L.266, M.269
- Ligands: BCR.40, CLA.41, CLA.45, CLA.46, CLA.49
12 PLIP interactions:12 interactions with chain C,- Hydrophobic interactions: C:M.144, C:T.145, C:L.155, C:W.246, C:F.251, C:F.251, C:W.253, C:Y.258, C:Y.261, C:Y.261, C:A.265, C:L.266
CLA.48: 24 residues within 4Å:- Chain C: F.20, W.23, S.24, G.25, N.26, A.27, E.256, L.259, L.263, F.423, I.424, I.426, G.427, W.430, H.431, R.434
- Chain J: L.28
- Ligands: CLA.44, CLA.49, CLA.50, CLA.52, LMG.59, LHG.64, SQD.69
18 PLIP interactions:17 interactions with chain C, 1 interactions with chain J,- Hydrophobic interactions: C:N.26, C:A.27, C:L.259, C:L.259, C:L.263, C:F.423, C:I.424, C:I.426, C:W.430, J:L.28
- Hydrogen bonds: C:N.26, C:N.26, C:A.27
- Salt bridges: C:H.431, C:R.434
- pi-Stacking: C:W.430, C:H.431
- Metal complexes: C:H.431
CLA.49: 22 residues within 4Å:- Chain C: N.26, L.29, I.30, L.36, A.39, H.40, H.43, Y.136, W.138, H.151, G.255, E.256, Y.258, L.259, S.262, L.266
- Ligands: CLA.43, CLA.47, CLA.48, CLA.50, CLA.51, CLA.52
10 PLIP interactions:10 interactions with chain C,- Hydrophobic interactions: C:I.30, C:L.36, C:A.39, C:H.43, C:Y.136, C:W.138, C:Y.258
- Hydrogen bonds: C:S.262
- pi-Stacking: C:H.40
- Metal complexes: C:H.40
CLA.50: 17 residues within 4Å:- Chain C: N.26, H.43, L.46, I.47, W.50, L.266, L.420, F.423
- Chain J: P.24, L.28
- Ligands: CLA.42, CLA.43, CLA.44, CLA.48, CLA.49, CLA.52, LHG.64
9 PLIP interactions:7 interactions with chain C, 2 interactions with chain J,- Hydrophobic interactions: C:L.46, C:I.47, C:W.50, C:F.423, J:P.24, J:L.28
- Hydrogen bonds: C:N.26
- pi-Stacking: C:H.43
- Metal complexes: C:H.43
CLA.51: 17 residues within 4Å:- Chain C: L.37, H.40, A.44, L.112, F.133, F.134, I.147, I.150, H.151, L.154, I.157, G.158
- Ligands: CLA.41, CLA.43, CLA.49, CLA.53, BCR.75
11 PLIP interactions:11 interactions with chain C,- Hydrophobic interactions: C:L.37, C:H.40, C:F.134, C:I.147, C:I.147, C:I.150, C:I.150, C:I.157
- pi-Stacking: C:H.151, C:H.151
- Metal complexes: C:H.151
CLA.52: 25 residues within 4Å:- Chain C: G.12, R.13, W.22, W.23, G.25, N.26, R.28, L.32, K.35, A.39, L.46, I.117, S.120, I.121
- Chain J: F.27, A.31, W.34, Q.35
- Chain Q: I.24, L.27
- Ligands: CLA.48, CLA.49, CLA.50, BCR.60, BCR.74
12 PLIP interactions:2 interactions with chain Q, 6 interactions with chain J, 4 interactions with chain C,- Hydrophobic interactions: Q:I.24, Q:L.27, J:F.27, J:A.31, J:W.34, C:L.46, C:I.117, C:I.121
- pi-Stacking: J:W.34, J:W.34, J:W.34
- Hydrogen bonds: C:R.28
CLA.53: 14 residues within 4Å:- Chain C: L.37, V.41, V.111, L.112, F.114, G.115, Y.118, H.119, P.124, L.127, F.131, F.134
- Ligands: CLA.51, BCR.75
15 PLIP interactions:15 interactions with chain C,- Hydrophobic interactions: C:L.37, C:V.41, C:V.111, C:L.112, C:F.114, C:L.127, C:F.131, C:F.131, C:F.134
- Hydrogen bonds: C:Y.118
- Salt bridges: C:H.119
- pi-Stacking: C:Y.118, C:H.119, C:H.119
- Metal complexes: C:H.119
CLA.62: 28 residues within 4Å:- Chain A: M.183, F.206
- Chain D: L.44, W.47, L.121, P.148, V.151, S.154, V.155, F.180, L.181, L.184, Q.185, W.190, T.191, H.196, G.199, V.200, I.203, L.204, S.281, S.282, I.285
- Ligands: CLA.3, CLA.4, CLA.6, LMG.66, PHO.67
17 PLIP interactions:16 interactions with chain D, 1 interactions with chain A,- Hydrophobic interactions: D:L.44, D:W.47, D:L.121, D:V.151, D:F.180, D:L.184, D:Q.185, D:T.191, D:V.200, D:V.200, D:I.203, D:I.203, D:L.204, A:F.206
- pi-Stacking: D:W.190, D:H.196
- Metal complexes: D:H.196
CLA.63: 16 residues within 4Å:- Chain D: P.38, C.39, L.42, L.88, L.89, F.90, L.91, W.92, W.103, T.111, F.112, L.115, H.116, F.119
- Chain R: L.18
- Ligands: CLA.23
13 PLIP interactions:12 interactions with chain D, 1 interactions with chain R,- Hydrophobic interactions: D:P.38, D:L.42, D:F.90, D:W.92, D:W.92, D:W.92, D:F.112, D:L.115, D:F.119, R:L.18
- Hydrogen bonds: D:L.91
- Salt bridges: D:H.116
- Metal complexes: D:H.116
- 1 x OEX: CA-MN4-O5 CLUSTER(Non-covalent)
OEX.7: 11 residues within 4Å:- Chain A: Q.165, D.170, V.185, E.189, H.332, E.333, H.337, D.342, A.344
- Chain C: E.341, R.344
12 PLIP interactions:4 interactions with chain C, 7 interactions with chain A, 1 Ligand-Water interactions- Hydrogen bonds: C:R.344, C:R.344
- Metal complexes: C:E.341, C:E.341, A:D.170, A:E.189, A:H.332, A:E.333, A:E.333, A:D.342, A:D.342, H2O.1
- 2 x PHO: PHEOPHYTIN A(Non-covalent)
PHO.8: 26 residues within 4Å:- Chain A: L.41, A.44, T.45, F.48, V.115, Y.126, E.130, A.146, F.147, P.150, F.158, L.174, G.175, P.279, I.283
- Chain D: L.204, A.207, L.208, A.211, I.212, W.252, F.256
- Ligands: CLA.3, CLA.6, LHG.65, PL9.68
14 PLIP interactions:10 interactions with chain A, 4 interactions with chain D- Hydrophobic interactions: A:L.41, A:A.44, A:F.48, A:V.115, A:A.146, A:F.147, A:P.150, A:F.158, A:I.283, A:I.283, D:L.204, D:A.207, D:L.208, D:A.211
PHO.67: 28 residues within 4Å:- Chain A: F.206, A.209, L.210, M.214, F.255, L.258, I.259
- Chain D: W.47, T.113, G.117, G.120, L.121, F.124, Q.128, N.141, A.144, F.145, P.148, F.152, F.172, G.173, V.174, I.203, P.274, V.275, L.278
- Ligands: CLA.4, CLA.62
20 PLIP interactions:16 interactions with chain D, 4 interactions with chain A- Hydrophobic interactions: D:W.47, D:W.47, D:T.113, D:F.124, D:F.124, D:F.124, D:A.144, D:F.152, D:F.172, D:I.203, D:P.274, D:L.278, D:L.278, A:F.206, A:A.209, A:L.210, A:L.210
- Hydrogen bonds: D:Q.128, D:N.141
- pi-Stacking: D:F.145
- 5 x UNL: UNKNOWN LIGAND
UNL.9: 4 residues within 4Å:- Chain A: I.49, I.53, A.54
- Chain N: I.11
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain N- Hydrophobic interactions: A:I.49, A:I.53, A:A.54, N:I.11
UNL.36: 5 residues within 4Å:- Chain B: L.29, S.36, F.108
- Ligands: BCR.14, BCR.15
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.29, B:F.108, B:F.108
UNL.37: 4 residues within 4Å:- Chain B: A.228, R.230
- Ligands: CLA.23, CLA.24
No protein-ligand interaction detected (PLIP)UNL.38: 2 residues within 4Å:- Chain B: S.36, L.39
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:L.39
UNL.70: 3 residues within 4Å:- Chain D: S.32, L.126, E.130
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:L.126, D:E.130
- 7 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
LMG.10: 18 residues within 4Å:- Chain A: L.36, L.93, W.97, E.98
- Chain C: L.201, K.202, S.203, P.204, W.210
- Chain H: K.5, Y.9, C.16, F.19
- Chain S: L.8
- Ligands: CLA.5, CLA.45, CLA.46, DGD.55
8 PLIP interactions:5 interactions with chain H, 2 interactions with chain A, 1 interactions with chain C- Hydrophobic interactions: H:F.19, A:L.36, C:P.204
- Hydrogen bonds: H:K.5, H:K.5, H:Y.9, H:Y.9, A:W.97
LMG.12: 10 residues within 4Å:- Chain A: A.100, S.101, L.102
- Chain H: M.1, T.3, L.4, F.7
- Chain M: K.146
- Ligands: BCR.1, CLA.5
5 PLIP interactions:2 interactions with chain H, 1 interactions with chain A, 2 interactions with chain M- Hydrophobic interactions: H:L.4, H:F.7
- Hydrogen bonds: A:L.102, M:K.146, M:K.146
LMG.35: 12 residues within 4Å:- Chain B: P.88, G.89, L.90, W.91, L.149, F.162
- Chain T: W.3, F.4, V.6, S.7
- Ligands: BCR.16, CLA.22
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain T- Hydrophobic interactions: B:L.149, T:V.6
- Hydrogen bonds: B:L.90, B:W.91, T:S.7, T:S.7
LMG.39: 7 residues within 4Å:- Chain B: W.75, S.86, N.87, P.88, V.102
- Ligands: BCR.15, GOL.33
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:V.102
- Hydrogen bonds: B:W.75, B:S.86
LMG.59: 13 residues within 4Å:- Chain C: F.57, H.61, Q.71
- Chain J: D.18, I.19, V.22, L.29
- Chain Q: Q.9, L.13
- Ligands: CLA.42, CLA.44, CLA.48, DGD.54
6 PLIP interactions:2 interactions with chain J, 2 interactions with chain Q, 2 interactions with chain C- Hydrophobic interactions: J:I.19, J:L.29, Q:L.13
- Hydrogen bonds: Q:Q.9, C:H.61
- Salt bridges: C:H.61
LMG.66: 17 residues within 4Å:- Chain D: F.48, Y.66, G.69, C.70, N.71, F.72
- Chain F: I.35, M.38, Q.39
- Chain I: F.27, G.30, S.31, L.35, G.36
- Ligands: DGD.56, BCR.61, CLA.62
11 PLIP interactions:7 interactions with chain D, 2 interactions with chain I, 2 interactions with chain F- Hydrophobic interactions: D:F.48, D:F.72, D:F.72, D:F.72, D:F.72
- Hydrogen bonds: D:Y.66, D:F.72, I:F.27, I:G.30, F:M.38, F:Q.39
LMG.78: 11 residues within 4Å:- Chain B: A.327, G.328, F.453, F.458, L.461
- Chain K: F.36
- Chain L: Q.72, G.75
- Ligands: BCR.14, BCR.15, CLA.32
6 PLIP interactions:3 interactions with chain B, 1 interactions with chain L, 2 interactions with chain K- Hydrophobic interactions: B:F.458, B:L.461, K:F.36, K:F.36
- Hydrogen bonds: B:G.328, L:G.75
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 4 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
LHG.34: 23 residues within 4Å:- Chain A: S.232, N.234
- Chain B: W.5, Y.6, R.7, L.461, F.464, W.468
- Chain D: Y.140, I.143, W.265, F.268, F.272, V.275, T.276, W.279, V.280, I.283
- Chain K: L.24
- Ligands: CLA.26, CLA.28, PL9.68, LHG.76
20 PLIP interactions:8 interactions with chain B, 8 interactions with chain D, 2 interactions with chain A, 2 interactions with chain K- Hydrophobic interactions: B:W.5, B:W.5, B:Y.6, B:L.461, B:F.464, B:F.464, D:F.272, D:F.272, D:F.272, D:V.275, D:T.276, D:V.280, D:I.283, K:L.24, K:L.24
- Hydrogen bonds: B:Y.6, D:R.138, A:S.232, A:N.234
- Salt bridges: B:R.7
LHG.64: 21 residues within 4Å:- Chain A: R.140, W.142, F.273, G.276, L.277, W.278
- Chain C: F.20, W.23, S.24, W.430, R.434
- Chain D: E.218, N.219, S.228, T.230, F.231
- Ligands: CLA.44, CLA.48, CLA.50, DGD.56, SQD.69
10 PLIP interactions:3 interactions with chain C, 4 interactions with chain D, 3 interactions with chain A- Hydrogen bonds: C:S.24, C:S.24, C:R.434, D:N.219, D:S.228, D:T.230, D:F.231
- Hydrophobic interactions: A:F.273, A:L.277
- Salt bridges: A:R.140
LHG.65: 20 residues within 4Å:- Chain A: M.37
- Chain D: I.255, F.256, V.258, A.259, F.260, A.261, N.262, W.265
- Chain K: N.14, T.16, F.19, W.20
- Chain N: I.17, A.20, I.21
- Ligands: CLA.6, PHO.8, PL9.68, LHG.76
14 PLIP interactions:2 interactions with chain N, 5 interactions with chain K, 7 interactions with chain D- Hydrophobic interactions: N:I.17, N:I.21, K:W.20, K:W.20, K:W.20, D:F.256, D:F.256, D:F.256, D:V.258, D:F.260
- Hydrogen bonds: K:N.14, K:N.14, D:A.261, D:N.262
LHG.76: 20 residues within 4Å:- Chain A: S.232, N.234
- Chain B: P.4, W.5, Y.6
- Chain D: W.265, F.272
- Chain K: E.12, L.13, N.14, S.17, W.20, G.21, L.24
- Ligands: CLA.6, CLA.26, CLA.29, LHG.34, LHG.65, PL9.68
12 PLIP interactions:5 interactions with chain K, 2 interactions with chain D, 2 interactions with chain B, 3 interactions with chain A- Hydrophobic interactions: K:W.20, K:L.24, D:W.265, D:F.272, B:W.5
- Hydrogen bonds: K:E.12, K:N.14, K:S.17, B:W.5, A:S.232, A:S.232, A:N.234
- 4 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
DGD.54: 18 residues within 4Å:- Chain A: H.195, F.197, T.292
- Chain C: E.70, Q.71, G.72, L.391, S.393, N.405, Y.406, V.407, W.412, S.416
- Chain I: I.28, Y.32
- Ligands: CLA.44, DGD.56, LMG.59
12 PLIP interactions:7 interactions with chain C, 2 interactions with chain I, 3 interactions with chain A- Hydrophobic interactions: C:L.391, C:W.412, I:I.28, I:I.28, A:F.197, A:F.197, A:T.292
- Hydrogen bonds: C:S.393, C:N.405, C:V.407, C:V.407, C:W.412
DGD.55: 31 residues within 4Å:- Chain A: L.91, L.120, L.121, V.151, T.155, I.160, I.163
- Chain C: P.204, F.205, G.206, G.207, E.208, G.209, W.210, V.212, G.213, V.214, N.215, Q.271, E.275, Y.279, N.280, N.281, T.282, D.347, L.348, R.349, F.422, F.425
- Ligands: LMG.10, CLA.45
21 PLIP interactions:16 interactions with chain C, 5 interactions with chain A- Hydrophobic interactions: C:F.205, C:W.210, C:Q.271, C:E.275, C:F.422, C:F.422, C:F.425, C:F.425, A:L.120, A:L.121, A:V.151, A:T.155, A:I.163
- Hydrogen bonds: C:G.207, C:N.281, C:N.281, C:T.282, C:T.282, C:D.347, C:R.349, C:R.349
DGD.56: 22 residues within 4Å:- Chain A: P.196, M.199, A.203, N.301, F.302, S.305
- Chain C: L.391, N.392, V.394, N.402, S.403, N.405
- Chain D: L.73
- Chain I: S.31, Y.32, G.36, S.37, S.38
- Ligands: CLA.44, DGD.54, LHG.64, LMG.66
15 PLIP interactions:7 interactions with chain C, 3 interactions with chain A, 4 interactions with chain I, 1 interactions with chain D- Hydrophobic interactions: C:L.391, C:L.391, A:M.199, A:A.203, D:L.73
- Hydrogen bonds: C:N.392, C:N.402, C:N.402, C:S.403, C:V.404, A:S.305, I:S.31, I:Y.32, I:G.36, I:S.38
DGD.72: 27 residues within 4Å:- Chain B: F.250, G.254, Y.258, Y.273, Q.274, S.277, F.463
- Chain D: G.85, H.86, S.118, F.119, I.122, V.153, L.158, L.161, G.162, V.286, A.289, L.290
- Chain G: L.46, Y.49, N.50, I.60, S.61, W.62
- Ligands: CLA.18, CLA.23
20 PLIP interactions:5 interactions with chain G, 11 interactions with chain D, 4 interactions with chain B- Hydrophobic interactions: G:Y.49, G:Y.49, G:Y.49, D:S.118, D:F.119, D:V.153, D:L.158, D:L.161, D:V.286, D:A.289, D:L.290, B:Y.258, B:F.463
- Hydrogen bonds: G:N.50, G:I.60, D:H.86, D:H.86, B:Y.258, B:S.277
- Salt bridges: D:H.86
- 5 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)(Non-functional Binders)
LMT.58: 10 residues within 4Å:- Chain C: V.48, W.84, N.94, Y.96, P.97, T.101, I.104, H.105, S.108
- Ligands: CLA.43
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:V.48, C:I.104, C:I.104
LMT.77: 5 residues within 4Å:- Chain K: R.15, F.19
- Chain N: V.16
- Ligands: LMT.79, LMT.82
3 PLIP interactions:1 interactions with chain N, 2 interactions with chain K- Hydrophobic interactions: N:V.16, K:F.19, K:F.19
LMT.79: 3 residues within 4Å:- Chain L: I.91
- Ligands: LMT.77, LMT.82
No protein-ligand interaction detected (PLIP)LMT.80: 3 residues within 4Å:- Chain L: Y.76
- Chain N: M.1, F.8
5 PLIP interactions:3 interactions with chain N, 2 interactions with chain L- Hydrophobic interactions: N:F.8, N:F.8, L:Y.76
- Hydrogen bonds: N:M.1, L:Y.76
LMT.82: 2 residues within 4Å:- Ligands: LMT.77, LMT.79
No protein-ligand interaction detected (PLIP)- 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)
PL9.68: 31 residues within 4Å:- Chain A: F.48, F.52, I.77
- Chain D: M.198, A.201, G.202, L.208, L.209, H.213, T.216, Y.243, M.245, A.248, W.252, F.256, V.258, A.259, F.260, L.266, F.269, V.273, T.276
- Chain K: V.27, L.28, L.31
- Chain N: L.10
- Ligands: CLA.6, PHO.8, LHG.34, LHG.65, LHG.76
21 PLIP interactions:15 interactions with chain D, 3 interactions with chain A, 1 interactions with chain N, 2 interactions with chain K- Hydrophobic interactions: D:M.198, D:L.208, D:Y.243, D:A.248, D:W.252, D:F.256, D:F.260, D:F.260, D:L.266, D:F.269, D:V.273, D:V.273, A:F.48, A:F.52, A:I.77, N:L.10, K:L.28, K:L.31
- Hydrogen bonds: D:T.216, D:F.260
- pi-Stacking: D:F.260
- 1 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
- 2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.71: 8 residues within 4Å:- Chain E: H.24, I.28, L.31
- Chain F: W.18, H.22, A.25, I.26, V.29
8 PLIP interactions:5 interactions with chain F, 3 interactions with chain E,- Hydrophobic interactions: F:A.25, F:I.26, F:V.29, E:I.28, E:I.28
- pi-Stacking: F:W.18, F:H.22
- Metal complexes: E:H.24
HEM.83: 21 residues within 4Å:- Chain C: A.380
- Chain P: H.49, C.50, C.53, H.54, T.59, T.61, N.62, I.65, G.66, L.67, S.71, L.72, L.85, Y.88, M.89, Y.95, I.101, H.105, P.106, M.117
18 PLIP interactions:17 interactions with chain P, 1 interactions with chain C,- Hydrophobic interactions: P:H.49, P:T.59, P:T.61, P:N.62, P:I.65, P:L.67, P:L.72, P:L.85, P:Y.88, P:I.101, P:P.106, C:A.380
- Hydrogen bonds: P:N.62, P:G.66
- pi-Stacking: P:Y.88, P:H.105
- Metal complexes: P:H.54, P:H.105
- 1 x CA: CALCIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ago, H. et al., Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga. J.Biol.Chem. (2016)
- Release Date
- 2016-01-20
- Peptides
- Photosystem II protein D1: 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 J: I
Photosystem II reaction center protein K: J
Photosystem II reaction center protein L: K
PHOTOSYSTEM II REACTION CENTER PROTEIN M: L
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO: M
Photosystem II reaction center protein T: N
Photosystem II 12 kDa extrinsic protein, chloroplastic: O
Cytochrome c-550: P
Photosystem II reaction center protein Ycf12: Q
PHOTOSYSTEM II REACTION CENTER PROTEIN X: R
PEPTIDE CHAIN UNASSIGNED: S
PEPTIDE CHAIN UNASSIGNED: T - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A1B
B1C
C1D
D1E
E1F
F1G
H1H
I1I
J1J
K1K
L1L
M1M
O1N
T1O
U1P
V1Q
Y1R
X1S
S1T
W1 - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.77 Å
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 10 x BCR: BETA-CAROTENE(Non-covalent)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 35 x CLA: CHLOROPHYLL A(Non-covalent)
- 1 x OEX: CA-MN4-O5 CLUSTER(Non-covalent)
- 2 x PHO: PHEOPHYTIN A(Non-covalent)
- 5 x UNL: UNKNOWN LIGAND
- 7 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 4 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
- 4 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
- 5 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)(Non-functional Binders)
- 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)
- 1 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
- 2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ago, H. et al., Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga. J.Biol.Chem. (2016)
- Release Date
- 2016-01-20
- Peptides
- Photosystem II protein D1: 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 J: I
Photosystem II reaction center protein K: J
Photosystem II reaction center protein L: K
PHOTOSYSTEM II REACTION CENTER PROTEIN M: L
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO: M
Photosystem II reaction center protein T: N
Photosystem II 12 kDa extrinsic protein, chloroplastic: O
Cytochrome c-550: P
Photosystem II reaction center protein Ycf12: Q
PHOTOSYSTEM II REACTION CENTER PROTEIN X: R
PEPTIDE CHAIN UNASSIGNED: S
PEPTIDE CHAIN UNASSIGNED: T - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A1B
B1C
C1D
D1E
E1F
F1G
H1H
I1I
J1J
K1K
L1L
M1M
O1N
T1O
U1P
V1Q
Y1R
X1S
S1T
W1 - Membrane
-
We predict this structure to be a membrane protein.