- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 1 x FE2: FE (II) ION(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- 35 x CLA: CHLOROPHYLL A(Non-covalent)
- 2 x PHO: PHEOPHYTIN A(Non-covalent)
PHO.8: 27 residues within 4Å:- Chain A: L.41, A.44, T.45, F.48, I.115, F.119, Y.126, Q.130, A.146, Y.147, P.150, F.158, M.172, G.175, V.205, P.279, V.283
- Chain D: L.195, A.198, L.199, A.202, I.203, W.243, F.247
- Ligands: CLA.5, CLA.6, LHG.79
17 PLIP interactions:15 interactions with chain A, 2 interactions with chain D- Hydrophobic interactions: A:L.41, A:A.44, A:F.48, A:I.115, A:F.119, A:A.146, A:Y.147, A:Y.147, A:P.150, A:F.158, A:V.205, A:P.279, A:V.283, D:L.195, D:A.202
- Hydrogen bonds: A:Q.130, A:Y.147
PHO.19: 30 residues within 4Å:- Chain A: F.206, A.209, L.210, A.213, M.214, L.258, I.259
- Chain D: L.27, A.31, A.34, L.35, W.38, I.104, G.111, L.112, F.115, Q.119, N.132, A.135, F.136, P.139, F.143, G.164, V.165, P.265, V.266, L.269
- Ligands: CLA.7, PL9.16, CLA.74
22 PLIP interactions:18 interactions with chain D, 4 interactions with chain A- Hydrophobic interactions: D:A.31, D:W.38, D:W.38, D:W.38, D:W.38, D:I.104, D:L.112, D:L.112, D:F.115, D:A.135, D:P.139, D:F.143, D:V.165, D:P.265, D:L.269, A:F.206, A:A.209, A:L.210, A:A.213
- Hydrogen bonds: D:Q.119, D:N.132
- pi-Stacking: D:F.136
- 11 x BCR: BETA-CAROTENE(Non-covalent)
BCR.10: 16 residues within 4Å:- Chain A: V.35, I.38, L.42, A.43, I.46, C.47, I.50, A.51, A.55, I.96, W.105, L.106
- Chain H: F.15
- Ligands: CLA.9, UNL.17, UNL.92
11 PLIP interactions:2 interactions with chain H, 9 interactions with chain A- Hydrophobic interactions: H:F.15, H:F.15, A:V.35, A:I.38, A:L.42, A:L.42, A:I.46, A:A.51, A:I.96, A:W.105, A:L.106
BCR.38: 13 residues within 4Å:- Chain B: M.24, L.28, C.111, W.114
- Chain L: I.9, A.10, L.13
- Ligands: CLA.28, CLA.34, CLA.35, BCR.39, SQD.41, LMG.97
7 PLIP interactions:4 interactions with chain B, 3 interactions with chain L- Hydrophobic interactions: B:L.28, B:L.28, B:W.114, B:W.114, L:I.9, L:A.10, L:L.13
BCR.39: 15 residues within 4Å:- Chain B: L.28, G.31, W.32, S.35, I.100, V.101, S.103, G.104, L.108
- Ligands: CLA.28, CLA.32, CLA.34, BCR.38, SQD.41, LMG.97
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.28, B:W.32, B:I.100, B:L.108
BCR.40: 13 residues within 4Å:- Chain B: L.102, L.105, L.106, L.108, A.109, W.112, V.115, Y.116
- Ligands: CLA.26, CLA.27, CLA.36, CLA.37, UNL.47
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:L.102, B:L.105, B:L.106, B:V.115, B:Y.116
BCR.63: 15 residues within 4Å:- Chain C: F.94, V.98, I.102, S.103, V.106, L.107, F.129
- Chain J: Y.6
- Chain S: V.51, G.55, N.58, F.59
- Ligands: CLA.61, CLA.62, LMG.69
9 PLIP interactions:2 interactions with chain S, 7 interactions with chain C- Hydrophobic interactions: S:N.58, S:F.59, C:F.94, C:V.98, C:I.102, C:V.106, C:V.106, C:L.107, C:F.129
BCR.64: 20 residues within 4Å:- Chain C: I.191, F.192, Y.194, L.195, I.206, V.209, D.214, V.215, G.218, H.219, I.222, F.246
- Chain H: V.20, F.23, L.24
- Ligands: CLA.9, CLA.50, CLA.54, CLA.55, CLA.56
11 PLIP interactions:9 interactions with chain C, 2 interactions with chain H- Hydrophobic interactions: C:I.191, C:F.192, C:Y.194, C:L.195, C:I.206, C:V.209, C:I.222, C:I.222, C:F.246, H:F.23, H:L.24
BCR.76: 16 residues within 4Å:- Chain D: Y.32, L.33, G.36, G.37, L.39, T.40, F.91, F.103
- Chain F: P.28, T.29, F.32, L.33, I.36
- Chain I: V.20, V.24
- Ligands: LMG.84
13 PLIP interactions:2 interactions with chain I, 6 interactions with chain F, 5 interactions with chain D- Hydrophobic interactions: I:V.20, I:V.24, F:P.28, F:T.29, F:F.32, F:F.32, F:L.33, F:I.36, D:Y.32, D:L.39, D:F.91, D:F.103, D:F.103
BCR.90: 18 residues within 4Å:- Chain G: M.30, F.33, M.34, L.36, F.37, V.39, F.40, I.43, L.54
- Chain Q: T.1, I.2, L.6, F.10
- Ligands: CLA.22, CLA.23, CLA.24, CLA.30, CLA.31
10 PLIP interactions:8 interactions with chain G, 2 interactions with chain Q- Hydrophobic interactions: G:F.33, G:F.37, G:F.37, G:F.37, G:F.37, G:V.39, G:F.40, G:L.54, Q:L.6, Q:F.10
BCR.95: 19 residues within 4Å:- Chain C: A.37, G.40, L.41, F.44, F.94, L.101, I.102, S.104, A.105, G.108, A.115
- Chain J: Y.6, F.9, L.16, F.23
- Chain S: L.9, S.16
- Ligands: CLA.60, BCR.107
14 PLIP interactions:7 interactions with chain C, 1 interactions with chain S, 6 interactions with chain J- Hydrophobic interactions: C:A.37, C:L.41, C:F.44, C:F.94, C:I.102, C:A.105, C:A.115, S:L.9, J:Y.6, J:Y.6, J:F.9, J:L.16, J:F.23, J:F.23
BCR.103: 11 residues within 4Å:- Chain A: L.28
- Chain N: F.8, A.11, I.14, A.15, F.17, F.18, I.21, F.22
- Ligands: SQD.13, LMT.101
8 PLIP interactions:7 interactions with chain N, 1 interactions with chain A- Hydrophobic interactions: N:F.8, N:I.14, N:F.17, N:F.18, N:F.18, N:F.22, N:F.22, A:L.28
BCR.107: 26 residues within 4Å:- Chain C: F.44
- Chain I: A.13, T.14, G.17, M.18
- Chain J: L.12, L.16, I.19, L.22, A.25, L.26, F.28, V.29, A.32, F.36
- Chain R: I.12, G.13, G.16, P.17
- Chain S: V.13, S.16, F.17, V.20
- Ligands: SQD.11, UNL.73, BCR.95
13 PLIP interactions:9 interactions with chain J, 2 interactions with chain S, 1 interactions with chain R, 1 interactions with chain C- Hydrophobic interactions: J:L.12, J:I.19, J:I.19, J:L.22, J:A.25, J:L.26, J:V.29, J:A.32, J:F.36, S:F.17, S:V.20, R:P.17, C:F.44
- 4 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
SQD.11: 23 residues within 4Å:- Chain A: L.200, A.203, F.265, N.267, S.270, F.273, A.277, W.278, V.281, G.282
- Chain C: Q.10, A.16, W.17, W.18
- Chain D: S.220, F.222, R.223
- Chain J: F.28
- Ligands: CLA.57, LMG.68, UNL.73, LHG.80, BCR.107
15 PLIP interactions:2 interactions with chain D, 1 interactions with chain J, 9 interactions with chain A, 3 interactions with chain C- Hydrogen bonds: D:S.220, A:N.267, A:S.270, C:Q.10
- Salt bridges: D:R.223
- Hydrophobic interactions: J:F.28, A:A.203, A:F.265, A:A.277, A:W.278, A:W.278, C:W.17, C:W.18
- Water bridges: A:N.266, A:S.270
SQD.13: 11 residues within 4Å:- Chain A: W.20, N.26, R.27, L.28, I.38, L.42
- Chain N: F.22
- Ligands: CLA.6, UNL.17, UNL.92, BCR.103
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:N.26, A:I.38, A:I.38, A:L.42
- Hydrogen bonds: A:W.20, A:R.27, A:L.28
SQD.41: 9 residues within 4Å:- Chain B: R.17, L.28, S.103, F.107, W.114
- Chain K: R.7
- Ligands: CLA.35, BCR.38, BCR.39
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain K- Hydrophobic interactions: B:L.28, B:F.107
- Salt bridges: B:R.17, K:R.7
- Hydrogen bonds: K:R.7, K:R.7
SQD.88: 14 residues within 4Å:- Chain D: R.16
- Chain E: E.7
- Chain F: I.14, F.15, T.16, V.17, V.20
- Chain Q: T.23, V.26, L.27, I.30, D.34
- Ligands: PL9.16, CLA.75
8 PLIP interactions:4 interactions with chain F, 1 interactions with chain D, 3 interactions with chain Q- Hydrophobic interactions: F:F.15, F:F.15, Q:V.26, Q:L.27, Q:I.30
- Hydrogen bonds: F:F.15, F:V.17
- Salt bridges: D:R.16
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.12: 2 residues within 4Å:- Chain A: D.103, L.106
1 PLIP interactions:1 interactions with chain M- Water bridges: M:Q.107
GOL.18: 10 residues within 4Å:- Chain A: G.74, N.75, N.76
- Chain D: S.290, Q.291
- Chain K: N.37
- Chain L: M.1, V.3
- Chain N: E.2, Y.6
8 PLIP interactions:3 interactions with chain N, 3 interactions with chain D, 1 interactions with chain K, 1 interactions with chain A- Hydrogen bonds: N:E.2, N:E.2, N:Y.6, D:S.290, D:S.290, D:Q.291, A:N.76
- Water bridges: K:N.37
GOL.45: 8 residues within 4Å:- Chain B: I.12, N.13, P.130, A.131, L.132, G.231, N.232, I.233
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:N.13, B:L.132, B:I.233
- Water bridges: B:N.232
GOL.49: 10 residues within 4Å:- Chain A: L.341, L.343
- Chain C: M.378, T.379, H.380, A.381, G.391, V.392, E.395
- Chain P: K.47
7 PLIP interactions:5 interactions with chain C, 2 interactions with chain P- Hydrogen bonds: C:M.378, C:A.381, C:V.392, C:E.395, P:K.47
- Water bridges: C:T.379, P:K.47
GOL.104: 7 residues within 4Å:- Chain A: L.341
- Chain C: V.392
- Chain O: K.104
- Chain P: I.45, G.133, K.134, Y.137
2 PLIP interactions:1 interactions with chain O, 1 interactions with chain P- Water bridges: O:K.104
- Hydrogen bonds: P:K.134
- 8 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.14: 6 residues within 4Å:- Chain A: I.53, L.72, Y.73
- Chain D: R.294
- Chain M: G.110
- Ligands: LMT.101
6 PLIP interactions:2 interactions with chain D, 3 interactions with chain A, 1 interactions with chain M- Hydrogen bonds: D:R.294, D:R.294, A:Y.73, M:G.110
- Hydrophobic interactions: A:I.53, A:L.72
LMT.21: 9 residues within 4Å:- Chain A: N.12, W.14, E.15
- Chain C: W.241, R.244
- Chain H: L.24, S.25, G.26, R.30
9 PLIP interactions:3 interactions with chain C, 4 interactions with chain H, 2 interactions with chain A- Hydrophobic interactions: C:W.241, H:L.24
- Hydrogen bonds: C:R.244, C:R.244, H:S.25, H:R.30, A:N.12, A:E.15
- Water bridges: H:R.30
LMT.42: 12 residues within 4Å:- Chain B: R.223, L.224, K.226, A.227, K.497
- Chain D: F.5, D.6, D.9
- Chain G: W.24, M.30, M.34
- Ligands: UNL.82
10 PLIP interactions:2 interactions with chain D, 2 interactions with chain G, 6 interactions with chain B- Hydrophobic interactions: D:F.5, G:W.24, G:W.24, B:L.224, B:A.227
- Hydrogen bonds: D:D.6, B:R.223, B:K.226
- Salt bridges: B:R.223, B:K.226
LMT.48: 2 residues within 4Å:- Chain B: A.42, T.43
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:A.42
LMT.86: 6 residues within 4Å:- Chain E: F.31, W.35, S.39
- Chain F: F.41, I.42, Q.43
6 PLIP interactions:3 interactions with chain E, 3 interactions with chain F- Hydrophobic interactions: E:F.31, F:F.41
- Hydrogen bonds: E:S.39, E:S.39, F:Q.43, F:Q.43
LMT.99: 6 residues within 4Å:- Chain L: V.27, E.30, S.31, Q.32, Q.33, K.34
4 PLIP interactions:4 interactions with chain L- Hydrogen bonds: L:E.30, L:Q.32, L:Q.33, L:K.34
LMT.101: 7 residues within 4Å:- Chain A: L.72
- Chain N: M.1, I.4, F.8
- Ligands: LMT.14, LMT.102, BCR.103
2 PLIP interactions:2 interactions with chain N- Water bridges: N:T.3, N:T.3
LMT.102: 6 residues within 4Å:- Chain L: L.8, A.12
- Chain N: M.1, I.4, F.8
- Ligands: LMT.101
5 PLIP interactions:2 interactions with chain L, 3 interactions with chain N- Hydrophobic interactions: L:L.8, L:A.12, N:I.4, N:F.8, N:F.8
- 1 x OEX: CA-MN4-O5 CLUSTER(Covalent)
OEX.15: 11 residues within 4Å:- Chain A: D.61, D.170, V.185, E.189, H.332, E.333, H.337, D.342, A.344
- Chain C: E.336, R.339
19 PLIP interactions:10 interactions with chain A, 5 interactions with chain C, 4 Ligand-Water interactions- Water bridges: A:D.61
- Metal complexes: A:D.170, A:D.170, A:E.189, A:H.332, A:E.333, A:E.333, A:D.342, A:D.342, A:A.344, C:E.336, C:E.336, C:E.336, H2O.1, H2O.1, H2O.2, H2O.5
- Hydrogen bonds: C:R.339, C:R.339
- 2 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)
PL9.16: 29 residues within 4Å:- Chain A: F.211, M.214, H.215, L.218, I.248, A.251, H.252, F.255, I.259, A.263, S.264, F.265, L.271, F.274
- Chain D: V.20, F.28, L.35
- Chain F: V.17, A.21, T.24, L.25
- Chain Q: T.23, L.27
- Ligands: CLA.7, PHO.19, CLA.74, CLA.75, LHG.85, SQD.88
24 PLIP interactions:16 interactions with chain A, 2 interactions with chain F, 4 interactions with chain D, 2 interactions with chain Q- Hydrophobic interactions: A:F.211, A:F.211, A:M.214, A:L.218, A:I.248, A:A.251, A:H.252, A:F.255, A:F.255, A:I.259, A:F.265, A:L.271, A:L.271, A:F.274, F:V.17, F:L.25, D:V.20, D:F.28, D:F.28, D:L.35, Q:T.23, Q:L.27
- Hydrogen bonds: A:H.215, A:F.265
PL9.77: 34 residues within 4Å:- Chain A: F.52, I.53, I.77, I.176
- Chain D: M.188, M.189, A.192, G.193, L.199, I.203, H.204, T.207, Y.234, M.236, A.239, N.240, W.243, I.249, A.250, F.251, L.257, F.260, F.263, V.264, G.268
- Chain K: L.23, V.26, L.27, L.29
- Chain N: F.10
- Ligands: CLA.6, CLA.28, LHG.79, LHG.96
27 PLIP interactions:16 interactions with chain D, 4 interactions with chain A, 4 interactions with chain N, 3 interactions with chain K- Hydrophobic interactions: D:M.188, D:M.189, D:L.199, D:I.203, D:T.207, D:Y.234, D:W.243, D:F.251, D:F.251, D:L.257, D:F.260, D:F.263, D:V.264, A:F.52, A:I.53, A:I.77, A:I.176, N:F.10, N:F.10, N:F.10, N:F.10, K:L.23, K:L.27, K:L.29
- Hydrogen bonds: D:T.207, D:F.251
- pi-Stacking: D:F.251
- 9 x UNL: UNKNOWN LIGAND
UNL.17: 6 residues within 4Å:- Chain A: R.16, F.17, W.20
- Ligands: BCR.10, SQD.13, UNL.92
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:F.17, A:W.20, A:W.20, A:W.20, A:W.20
- Salt bridges: A:R.16
UNL.47: 7 residues within 4Å:- Chain B: W.90, L.148, F.161
- Ligands: CLA.25, CLA.26, CLA.27, BCR.40
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:L.148, B:F.161
UNL.73: 7 residues within 4Å:- Chain C: W.17
- Chain D: R.223
- Chain J: F.28, F.36
- Ligands: SQD.11, LHG.80, BCR.107
6 PLIP interactions:1 interactions with chain D, 3 interactions with chain J, 2 interactions with chain C- Hydrogen bonds: D:R.223
- Hydrophobic interactions: J:F.28, J:F.36, J:F.36, C:W.17, C:W.17
UNL.81: 7 residues within 4Å:- Chain D: W.22, S.23, I.25, L.117, F.120
- Chain Q: L.20
- Ligands: UNL.82
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain Q- Hydrophobic interactions: D:I.25, D:L.117, Q:L.20
UNL.82: 9 residues within 4Å:- Chain B: A.227, R.229
- Chain D: D.9, K.13, W.22
- Ligands: CLA.29, CLA.30, LMT.42, UNL.81
5 PLIP interactions:2 interactions with chain D, 3 interactions with chain B- Hydrophobic interactions: D:W.22, B:A.227
- Salt bridges: D:K.13
- Hydrogen bonds: B:R.229, B:R.229
UNL.92: 8 residues within 4Å:- Chain H: M.1, T.3, L.4, T.7
- Ligands: CLA.9, BCR.10, SQD.13, UNL.17
3 PLIP interactions:3 interactions with chain H- Hydrophobic interactions: H:L.4, H:T.7
- Hydrogen bonds: H:T.3
UNL.93: 4 residues within 4Å:- Chain I: G.25, Y.29
- Ligands: DGD.66, LMG.68
No protein-ligand interaction detected (PLIP)UNL.98: 1 residues within 4Å:- Chain L: I.23
1 PLIP interactions:1 interactions with chain L- Hydrophobic interactions: L:I.23
UNL.106: 7 residues within 4Å:- Chain D: L.82, W.83, G.89
- Chain Q: S.15, G.16, L.20
- Ligands: CLA.75
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain Q- Hydrophobic interactions: D:L.82, D:W.83, Q:L.20
- 6 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
LMG.20: 17 residues within 4Å:- Chain A: F.93, W.97, E.98, F.117
- Chain C: L.195, L.196, K.197, S.198, F.200, E.203, W.205, F.266
- Chain H: K.5, Y.9
- Ligands: CLA.9, CLA.54, DGD.65
13 PLIP interactions:4 interactions with chain H, 4 interactions with chain A, 5 interactions with chain C- Hydrogen bonds: H:K.5, H:K.5, H:Y.9, H:Y.9, A:W.97, A:E.98, C:E.203
- Hydrophobic interactions: A:F.117, A:F.117, C:W.205, C:F.266
- Water bridges: C:S.198, C:S.198
LMG.68: 13 residues within 4Å:- Chain C: F.52, H.56, Q.66
- Chain I: I.21
- Chain J: D.14, V.18, V.21
- Chain R: Q.5
- Ligands: SQD.11, CLA.53, CLA.57, DGD.66, UNL.93
7 PLIP interactions:2 interactions with chain C, 3 interactions with chain J, 1 interactions with chain R, 1 interactions with chain I- Water bridges: C:H.56
- Salt bridges: C:H.56
- Hydrophobic interactions: J:V.18, J:V.18, J:V.21, I:I.21
- Hydrogen bonds: R:Q.5
LMG.69: 14 residues within 4Å:- Chain C: V.43, W.79, D.89, F.91, V.95, V.96, V.99, H.100, S.103
- Chain S: F.59, V.62
- Ligands: CLA.52, CLA.62, BCR.63
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:V.43, C:W.79, C:V.96, C:V.99
- Hydrogen bonds: C:D.89
LMG.84: 18 residues within 4Å:- Chain D: L.39, Y.57, G.60, C.61, N.62, F.63
- Chain F: T.29, I.36, M.39, Q.40
- Chain I: F.27, G.30, A.31, L.35
- Ligands: CLA.7, DGD.67, BCR.76, MG.94
9 PLIP interactions:3 interactions with chain I, 2 interactions with chain F, 4 interactions with chain D- Hydrogen bonds: I:G.30, F:M.39, F:Q.40, D:F.63
- Water bridges: I:F.27, I:G.36, D:N.62
- Hydrophobic interactions: D:L.39, D:F.63
LMG.97: 23 residues within 4Å:- Chain B: Y.39, T.326, G.327, P.328, K.331, F.452, A.453, V.456, L.460
- Chain D: I.274
- Chain K: F.35
- Chain L: N.4, L.6, A.10, F.14, V.17
- Ligands: CLA.28, CLA.34, CLA.35, BCR.38, BCR.39, LHG.78, LHG.96
14 PLIP interactions:7 interactions with chain B, 5 interactions with chain L, 1 interactions with chain K, 1 interactions with chain D- Hydrophobic interactions: B:F.452, B:A.453, B:V.456, B:L.460, L:A.10, L:F.14, L:V.17, K:F.35, D:I.274
- Hydrogen bonds: B:T.326, B:T.326, L:N.4
- Water bridges: B:T.326, L:N.4
LMG.108: 11 residues within 4Å:- Chain C: F.109, Y.113, R.117
- Chain S: M.19, Y.27, W.33, K.37, F.41, W.47
- Ligands: CLA.60, CLA.62
11 PLIP interactions:7 interactions with chain S, 4 interactions with chain C- Hydrophobic interactions: S:M.19, S:F.41, S:F.41, S:W.47, S:W.47, S:W.47, C:F.109, C:F.109
- Salt bridges: S:K.37
- Hydrogen bonds: C:Y.113, C:R.117
- 5 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
HTG.43: 5 residues within 4Å:- Chain B: S.73, S.75, W.77, E.93, L.97
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.97
- Hydrogen bonds: B:S.73, B:E.93
- Water bridges: B:L.41
HTG.44: 3 residues within 4Å:- Chain B: W.184, I.206
- Ligands: CLA.22
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:W.184, B:I.206, B:I.206
- Hydrogen bonds: B:W.184
HTG.46: 4 residues within 4Å:- Chain B: W.74, D.86, G.88, F.89
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.86, B:G.88, B:G.88
HTG.70: 4 residues within 4Å:- Chain C: W.79, F.163, F.164, G.165
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:W.79
HTG.83: 5 residues within 4Å:- Chain D: G.3, W.4, F.5
- Chain G: W.24, P.28
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:F.5
- 4 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
DGD.65: 34 residues within 4Å:- Chain A: L.91, S.148, L.151, A.152, F.155, L.159, I.160, I.163
- Chain C: P.199, F.200, G.201, G.202, E.203, G.204, W.205, V.207, S.208, V.209, N.210, M.263, F.266, C.270, F.274, N.275, N.276, T.277, D.342, F.343, R.344, L.420
- Ligands: CLA.9, LMG.20, CLA.54, CLA.55
23 PLIP interactions:18 interactions with chain C, 5 interactions with chain A- Hydrophobic interactions: C:P.199, C:F.200, C:W.205, C:V.207, C:F.266, C:F.266, C:L.420, A:L.151, A:F.155, A:F.155, A:L.159, A:I.160
- Hydrogen bonds: C:G.202, C:N.276, C:T.277, C:T.277, C:T.277, C:D.342, C:D.342, C:R.344, C:R.344
- Water bridges: C:F.200, C:N.210
DGD.66: 19 residues within 4Å:- Chain A: H.195, F.197
- Chain C: E.65, Q.66, G.67, L.386, S.388, N.400, F.401, V.402, W.407, T.410, S.411
- Chain I: Y.32
- Ligands: CLA.53, CLA.57, DGD.67, LMG.68, UNL.93
11 PLIP interactions:9 interactions with chain C, 1 interactions with chain A, 1 interactions with chain I- Hydrophobic interactions: C:L.386, A:F.197
- Hydrogen bonds: C:S.388, C:N.400, C:N.400, C:V.402, C:V.402
- Water bridges: C:E.65, C:G.67, C:G.67, I:Y.32
DGD.67: 28 residues within 4Å:- Chain A: P.196, Q.199, L.200, F.300, N.301, F.302, S.305
- Chain C: N.387, S.388, V.389, N.397, S.398, V.399, N.400
- Chain D: N.62
- Chain I: F.28, A.31, Y.32, G.36, S.37, S.38
- Chain P: Q.34
- Ligands: CLA.7, CLA.53, CLA.57, DGD.66, LHG.80, LMG.84
17 PLIP interactions:6 interactions with chain A, 4 interactions with chain I, 5 interactions with chain C, 2 interactions with chain P- Hydrophobic interactions: A:P.196, A:L.200, A:L.200, A:F.300, A:F.300
- Hydrogen bonds: A:S.305, I:G.36, I:S.38, C:N.387, C:N.397, C:S.398, C:V.399, P:Q.34, P:Q.34
- Water bridges: I:G.36, I:S.38, C:N.397
DGD.91: 29 residues within 4Å:- Chain B: Y.192, F.249, G.253, Y.257, Y.272, Q.273, S.276, Y.278, T.451, A.455, F.462
- Chain D: G.76, H.77, F.110, I.113, V.144, I.149, L.152, G.153, S.155, L.281
- Chain G: L.45, Y.48, N.49, V.59, S.60, W.61
- Ligands: CLA.23, CLA.29
23 PLIP interactions:8 interactions with chain D, 8 interactions with chain G, 7 interactions with chain B- Hydrophobic interactions: D:F.110, D:I.113, D:V.144, D:I.149, D:L.152, D:L.281, G:L.45, G:Y.48, G:Y.48, G:Y.48, B:Y.257, B:T.451, B:A.455, B:F.462
- Hydrogen bonds: D:H.77, D:S.155, G:N.49, G:V.59, G:S.60, G:W.61, B:Y.192, B:Q.273
- Water bridges: B:Y.192
- 4 x CA: CALCIUM ION(Non-covalent)
CA.71: 6 residues within 4Å:- Chain C: N.137, T.140, T.141, H.233, I.234, T.236
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:N.137, C:T.140, C:T.141, C:H.233, C:T.236
CA.72: 5 residues within 4Å:- Chain C: F.4, T.6, D.9, E.11, S.12
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:F.4, C:T.6, C:D.9, C:E.11, C:S.12
CA.89: 3 residues within 4Å:- Chain A: A.309
- Chain F: R.44
- Chain P: E.23
2 PLIP interactions:1 interactions with chain P, 1 Ligand-Water interactions- Metal complexes: P:E.23, H2O.23
CA.100: 3 residues within 4Å:- Chain M: T.136, N.198, V.199
3 PLIP interactions:2 interactions with chain M, 1 Ligand-Water interactions- Metal complexes: M:T.136, M:V.199, H2O.25
- 5 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
LHG.78: 23 residues within 4Å:- Chain A: N.234
- Chain B: W.4, Y.5, R.6, L.460, F.463, W.467, F.478
- Chain D: R.129, Y.131, I.134, W.256, F.259, F.263, T.267, M.271
- Chain K: L.23
- Chain L: P.18
- Ligands: CLA.28, CLA.32, CLA.34, LHG.96, LMG.97
12 PLIP interactions:4 interactions with chain D, 4 interactions with chain B, 1 interactions with chain L, 1 interactions with chain K, 2 interactions with chain A- Hydrophobic interactions: D:F.263, B:W.4, B:Y.5, B:L.460, L:P.18, K:L.23
- Hydrogen bonds: D:R.129, D:Y.131, A:N.234, A:N.234
- Water bridges: D:Y.131
- Salt bridges: B:R.6
LHG.79: 24 residues within 4Å:- Chain A: M.37
- Chain D: I.246, F.247, I.249, A.250, F.251, S.252, N.253, W.256, F.260
- Chain K: N.13, T.15, S.16, Y.18, L.19, L.22, L.29
- Chain N: F.17, A.20, I.21
- Ligands: CLA.5, PHO.8, PL9.77, LHG.96
18 PLIP interactions:7 interactions with chain D, 5 interactions with chain N, 6 interactions with chain K- Hydrophobic interactions: D:F.247, D:I.249, D:F.251, D:F.260, N:F.17, N:F.17, N:F.17, N:A.20, N:I.21, K:Y.18, K:L.22, K:L.29
- Hydrogen bonds: D:S.252, D:S.252, D:N.253, K:N.13, K:N.13, K:S.16
LHG.80: 21 residues within 4Å:- Chain A: R.140, W.142, A.146, F.273, V.280, F.285
- Chain C: W.18, W.425, R.429
- Chain D: E.209, N.210, A.219, S.220, T.221, F.222
- Ligands: SQD.11, CLA.53, CLA.57, CLA.59, DGD.67, UNL.73
13 PLIP interactions:5 interactions with chain C, 5 interactions with chain A, 3 interactions with chain D- Hydrophobic interactions: C:W.18, C:W.18, C:W.425, A:W.142, A:A.146, A:V.280, A:F.285
- Hydrogen bonds: C:R.429, C:R.429, D:N.210, D:A.219, D:T.221
- Salt bridges: A:R.140
LHG.85: 12 residues within 4Å:- Chain A: L.258, I.259, F.260, Y.262
- Chain D: F.17, F.28
- Chain E: E.7, P.9, F.10, S.11
- Chain F: R.18
- Ligands: PL9.16
9 PLIP interactions:2 interactions with chain A, 5 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D- Hydrophobic interactions: A:F.260, A:F.260, D:F.28
- Hydrogen bonds: E:E.7, E:E.7, E:F.10, E:S.11, E:S.11, F:R.18
LHG.96: 26 residues within 4Å:- Chain A: S.232, N.234
- Chain B: P.3, W.4, Y.5
- Chain D: W.256, F.263
- Chain K: E.11, L.12, N.13, S.16, L.19, G.20, L.22, L.23
- Chain L: V.17, P.18, F.21
- Ligands: CLA.6, CLA.32, CLA.34, CLA.35, PL9.77, LHG.78, LHG.79, LMG.97
15 PLIP interactions:3 interactions with chain L, 2 interactions with chain B, 4 interactions with chain K, 3 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: L:V.17, L:P.18, L:F.21, K:L.22, D:W.256, D:F.263, D:F.263
- Hydrogen bonds: B:W.4, B:Y.5, K:E.11, K:N.13, K:S.16, A:S.232, A:S.232, A:N.234
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.87: 17 residues within 4Å:- Chain E: R.8, F.10, I.13, R.18, Y.19, I.22, H.23, T.26, I.27, L.30
- Chain F: R.18, W.19, V.22, H.23, A.26, V.27, I.30
16 PLIP interactions:9 interactions with chain E, 7 interactions with chain F,- Hydrophobic interactions: E:F.10, E:I.22, E:T.26, E:I.27, E:I.27, F:V.22, F:A.26, F:I.30
- Hydrogen bonds: E:R.8
- Salt bridges: E:R.18, F:R.18
- pi-Stacking: E:Y.19, F:W.19, F:W.19
- Metal complexes: E:H.23, F:H.23
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x HEC: HEME C(Covalent)
HEC.105: 23 residues within 4Å:- Chain P: A.36, C.37, S.39, C.40, H.41, T.46, T.48, N.49, L.52, D.53, L.54, T.58, L.59, L.72, Y.75, M.76, T.81, Y.82, I.88, H.92, P.93, I.115, I.119
19 PLIP interactions:19 interactions with chain P,- Hydrophobic interactions: P:A.36, P:T.46, P:N.49, P:L.52, P:L.54, P:L.72, P:Y.75, P:Y.75, P:I.88, P:P.93, P:I.115, P:I.119
- Hydrogen bonds: P:D.53, P:D.53, P:Y.82
- Water bridges: P:N.49
- pi-Stacking: P:Y.75
- Metal complexes: P:H.41, P:H.92
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Suga, M. et al., Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL. Nature (2017)
- Release Date
- 2017-03-15
- Peptides
- Photosystem II D1 protein: A
Photosystem II CP47 reaction center protein: B
Photosystem II CP43 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 protein K: J
Photosystem II reaction center protein L: K
Photosystem II protein M: L
Photosystem II manganese-stabilizing polypeptide: M
Photosystem II reaction center protein T: N
Photosystem II 12 kDa extrinsic protein: O
Cytochrome c-550: P
Photosystem II reaction center protein X: Q
Photosystem II reaction center protein Ycf12: R
Photosystem II reaction center protein Z: S - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
aB
bC
cD
dE
eF
fG
hH
iI
jJ
kK
lL
mM
oN
tO
uP
vQ
xR
yS
z - Membrane
-
We predict this structure to be a membrane protein.
SMTL ID : 5ws5.2 (1 other biounit)
Native XFEL structure of photosystem II (preflash dark dataset)
Photosystem II D1 protein
Photosystem II CP47 reaction center protein
Photosystem II CP43 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 J
Photosystem II protein K
Photosystem II reaction center protein L
Photosystem II protein M
Photosystem II manganese-stabilizing polypeptide
Photosystem II reaction center protein T
Photosystem II 12 kDa extrinsic protein
Cytochrome c-550
Photosystem II reaction center protein X
Photosystem II reaction center protein Ycf12
Photosystem II reaction center protein Z
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1izl.1 | 1mz4.1 | 1s5l.1 | 1s5l.2 | 1w5c.1 | 1w5c.2 | 2axt.1 | 3a0b.1 | 3a0h.1 | 3kzi.1 | 3wu2.1 | 4fby.1 | 4il6.1 | 4ixq.1 | 4ixr.1 | 4pbu.1 | 4pj0.1 | 4rvy.1 | 4tnh.1 | 4tni.1 | 4tnj.1 | 4tnk.1 | 4ub6.1 | 4ub6.2 | 4ub8.1 | 4ub8.2 | 4v62.1 | 4v62.2 | 4v82.1 | 5b5e.1 more...less...5b66.1 | 5e79.1 | 5e7c.1 | 5gth.1 | 5gth.2 | 5gti.1 | 5gti.2 | 5h2f.1 | 5h2f.2 | 5kaf.1 | 5kai.1 | 5mx2.1 | 5mx2.2 | 5tis.1 | 5v2c.1 | 5ws5.1 | 5ws6.1 | 5ws6.2 | 5zzn.1 | 5zzn.2 | 6dhe.1 | 6dhf.1 | 6dhg.1 | 6dhh.1 | 6dho.1 | 6dhp.1 | 6jlj.1 | 6jlk.1 | 6jll.1 | 6jlm.1 | 6jln.1 | 6jlo.1 | 6jlp.1 | 6w1o.1 | 6w1p.1 | 6w1q.1 | 6w1r.1 | 6w1t.1 | 6w1u.1 | 6w1v.1 | 7cji.1 | 7cjj.1 | 7cou.1 | 7czl.1 | 7d1t.1 | 7d1u.1 | 7dxa.1 | 7dxh.1 | 7eda.1 | 7nho.1 | 7nhp.1 | 7nhq.1 | 7rf1.1 | 7rf2.1 | 7rf3.1 | 7rf4.1 | 7rf5.1 | 7rf6.1 | 7rf7.1 | 7rf8.1 | 7yq2.1 | 7yq7.1 | 8ez5.1 | 8f4c.1 | 8f4d.1 | 8f4e.1 | 8f4f.1 | 8f4g.1 | 8f4h.1 | 8f4i.1 | 8f4j.1 | 8f4k.1 | 8gn0.1 | 8gn1.1 | 8gn2.1 | 8ir5.1 | 8ir6.1 | 8ir7.1 | 8ir8.1 | 8ir9.1 | 8ira.1 | 8irb.1 | 8irc.1 | 8ird.1 | 8ire.1 | 8irf.1 | 8irg.1 | 8irh.1 | 8iri.1 | 9evx.1