- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 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
- 1 x FE2: FE (II) ION(Non-covalent)
- 3 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.7: 28 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, SQD.16, CLA.81, LHG.89
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:Y.126, A:Q.130
PHO.8: 33 residues within 4Å:- Chain A: F.206, A.209, L.210, M.214, F.255, L.258, I.259
- Chain D: 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, A.138, P.139, F.143, F.163, G.164, V.165, P.265, V.266, L.269
- Ligands: CLA.6, PL9.19, CLA.83
22 PLIP interactions:20 interactions with chain D, 2 interactions with chain A- Hydrophobic interactions: D:A.31, D:A.34, D:W.38, D:W.38, D:I.104, D:L.112, D:F.115, D:F.115, D:A.135, D:A.138, D:P.139, D:F.143, D:F.163, D:P.265, D:L.269, D:L.269, A:F.206, A:L.210
- Hydrogen bonds: D:Q.119, D:N.132
- pi-Stacking: D:F.136, D:F.136
- 11 x BCR: BETA-CAROTENE(Non-covalent)
BCR.10: 18 residues within 4Å:- Chain A: V.35, P.39, L.42, A.43, I.46, C.47, I.50, A.51, A.55, I.96, W.105, L.106
- Chain H: F.15, L.18
- Ligands: CLA.9, SQD.16, UNL.102, HTG.114
11 PLIP interactions:8 interactions with chain A, 3 interactions with chain H- Hydrophobic interactions: A:L.42, A:A.43, A:I.50, A:A.51, A:I.96, A:W.105, A:W.105, A:L.106, H:F.15, H:F.15, H:L.18
BCR.37: 9 residues within 4Å:- Chain B: M.24, L.28, W.114
- Chain L: A.10
- Ligands: CLA.27, CLA.33, CLA.34, BCR.38, LMG.40
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain L- Hydrophobic interactions: B:L.28, B:L.28, B:W.114, B:W.114, B:W.114, L:A.10
BCR.38: 14 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.27, CLA.31, CLA.33, BCR.37, LMG.40
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.28, B:W.32, B:I.100, B:L.108
BCR.39: 11 residues within 4Å:- Chain B: L.105, L.108, A.109, W.112, V.115, Y.116
- Ligands: CLA.25, CLA.26, CLA.35, CLA.36, UNL.51
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.108, B:W.112, B:V.115, B:Y.116
BCR.69: 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.67, CLA.68, LMG.75
10 PLIP interactions:7 interactions with chain C, 3 interactions with chain S- Hydrophobic interactions: C:F.94, C:V.98, C:I.102, C:V.106, C:V.106, C:L.107, C:F.129, S:V.51, S:N.58, S:F.59
BCR.70: 19 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: F.23, L.24
- Ligands: CLA.9, CLA.56, CLA.60, CLA.61, CLA.62
12 PLIP interactions:10 interactions with chain C, 2 interactions with chain H- Hydrophobic interactions: C:I.191, C:F.192, C:Y.194, C:Y.194, C:L.195, C:L.195, C:I.206, C:V.209, C:I.222, C:F.246, H:F.23, H:L.24
BCR.85: 17 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: DGD.87, LMG.104
13 PLIP interactions:5 interactions with chain F, 6 interactions with chain D, 2 interactions with chain I- Hydrophobic interactions: F:P.28, F:T.29, F:F.32, F:L.33, F:I.36, D:Y.32, D:L.33, D:L.39, D:F.91, D:F.103, D:F.103, I:V.20, I:V.24
BCR.100: 14 residues within 4Å:- Chain G: F.33, M.34, L.36, F.37, F.40, I.43, L.54
- Chain R: T.1, I.2, L.6
- Ligands: CLA.21, CLA.22, CLA.29, CLA.30
8 PLIP interactions:7 interactions with chain G, 1 interactions with chain R- Hydrophobic interactions: G:F.37, G:F.37, G:F.37, G:F.37, G:F.40, G:I.43, G:L.54, R:L.6
BCR.107: 17 residues within 4Å:- Chain C: A.37, G.40, L.41, F.44, L.101, S.104, A.105, G.108, A.115
- Chain J: Y.6, F.23, L.26
- Chain S: L.12, S.16
- Ligands: CLA.66, BCR.126, LMG.128
13 PLIP interactions:6 interactions with chain C, 5 interactions with chain J, 2 interactions with chain S- Hydrophobic interactions: C:A.37, C:L.41, C:F.44, C:F.44, C:A.105, C:A.115, J:Y.6, J:Y.6, J:F.23, J:F.23, J:L.26, S:L.12, S:L.12
BCR.116: 10 residues within 4Å:- Chain A: L.28
- Chain N: F.8, A.11, A.15, F.17, F.18, I.21, F.22
- Ligands: SQD.16, LHG.89
6 PLIP interactions:5 interactions with chain N, 1 interactions with chain A- Hydrophobic interactions: N:A.15, N:F.18, N:F.18, N:F.22, N:F.22, A:L.28
BCR.126: 21 residues within 4Å:- Chain C: F.44
- Chain I: A.13, T.14, G.17, M.18
- Chain J: I.19, L.22, F.23, A.25, L.26, F.28, V.29
- Chain Q: I.12, G.13, G.16, P.17
- Chain S: S.16, F.17
- Ligands: SQD.11, UNL.80, BCR.107
11 PLIP interactions:7 interactions with chain J, 2 interactions with chain Q, 1 interactions with chain S, 1 interactions with chain C- Hydrophobic interactions: J:I.19, J:I.19, J:L.22, J:F.23, J:A.25, J:L.26, J:V.29, Q:I.12, Q:P.17, S:F.17, C:F.44
- 3 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
SQD.11: 22 residues within 4Å:- Chain A: L.200, A.203, G.204, F.265, N.267, S.270, F.273, A.277, W.278, V.281, G.282
- Chain C: Q.10, A.16, W.18
- Chain D: F.222, R.223
- Chain J: A.25, F.28
- Ligands: CLA.63, UNL.80, LHG.90, BCR.126
20 PLIP interactions:12 interactions with chain A, 2 interactions with chain C, 3 interactions with chain J, 3 interactions with chain D- Hydrophobic interactions: A:A.203, A:F.265, A:F.273, A:A.277, A:W.278, A:W.278, A:W.278, A:V.281, C:W.18, J:A.25, J:F.28, J:F.28
- Hydrogen bonds: A:N.267, A:S.270, A:S.270, C:Q.10
- Water bridges: A:N.267, D:F.222, D:R.223
- Salt bridges: D:R.223
SQD.16: 15 residues within 4Å:- Chain A: W.20, N.26, R.27, L.28, V.30, I.38, L.42, T.45, I.46
- Chain N: F.22
- Ligands: PHO.7, BCR.10, CLA.81, UNL.102, BCR.116
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:L.28, A:V.30, A:I.38, A:L.42, A:I.46
- Hydrogen bonds: A:N.26, A:R.27, A:L.28
SQD.97: 15 residues within 4Å:- Chain D: R.14, R.16
- Chain F: F.15, T.16, V.17, V.20
- Chain R: T.23, L.27, I.30, D.34
- Chain T: Q.29, L.33
- Ligands: PL9.19, CLA.84, DGD.87
9 PLIP interactions:3 interactions with chain R, 2 interactions with chain D, 3 interactions with chain F, 1 interactions with chain T- Hydrophobic interactions: R:T.23, R:L.27, R:I.30, F:V.20
- Hydrogen bonds: D:R.14, F:V.17, T:Q.29
- Salt bridges: D:R.16
- Water bridges: F:R.18
- 21 x GOL: GLYCEROL(Non-functional Binders)
GOL.12: 5 residues within 4Å:- Chain A: P.56, D.103, L.106
- Chain M: Q.107
- Ligands: HTG.114
Ligand excluded by PLIPGOL.13: 8 residues within 4Å:- Chain A: G.74, N.75, N.76
- Chain D: S.290, Q.291
- Chain L: M.1, V.3
- Chain N: E.2
Ligand excluded by PLIPGOL.14: 7 residues within 4Å:- Chain A: V.313, N.315
- Chain D: W.48, G.52
- Chain E: Y.56, I.63
- Chain P: K.129
Ligand excluded by PLIPGOL.44: 7 residues within 4Å:- Chain B: W.274, D.275, R.356, R.357, M.358, P.359
- Chain D: E.327
Ligand excluded by PLIPGOL.45: 8 residues within 4Å:- Chain B: R.384, A.385, E.386, S.387, Q.393
- Chain O: L.17, Y.21, G.22
Ligand excluded by PLIPGOL.46: 9 residues within 4Å:- Chain B: I.12, P.15, P.130, A.131, L.132, G.231, N.232, I.233
- Chain G: Y.17
Ligand excluded by PLIPGOL.47: 8 residues within 4Å:- Chain B: P.49, P.53, M.54, I.79, T.80, W.166, E.265, K.307
Ligand excluded by PLIPGOL.48: 6 residues within 4Å:- Chain B: K.331, N.437, D.439
- Chain D: I.289
- Chain L: V.3, Q.5
Ligand excluded by PLIPGOL.52: 4 residues within 4Å:- Chain B: W.74, S.75
- Ligands: HTG.41, HTG.49
Ligand excluded by PLIPGOL.54: 4 residues within 4Å:- Chain B: Y.39
- Ligands: LMG.40, LMT.53, LMT.109
Ligand excluded by PLIPGOL.78: 6 residues within 4Å:- Chain C: I.301, R.302, K.305, E.371
- Chain P: N.49
- Ligands: HEC.120
Ligand excluded by PLIPGOL.79: 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
Ligand excluded by PLIPGOL.99: 6 residues within 4Å:- Chain A: A.309
- Chain F: R.44
- Chain P: L.3, E.23, L.27
- Ligands: CA.98
Ligand excluded by PLIPGOL.113: 3 residues within 4Å:- Chain M: P.18, R.40, Y.238
Ligand excluded by PLIPGOL.115: 6 residues within 4Å:- Chain D: S.252
- Chain K: T.15
- Chain N: R.24, E.25, P.27
- Ligands: LHG.89
Ligand excluded by PLIPGOL.117: 1 residues within 4Å:- Chain N: M.1
Ligand excluded by PLIPGOL.118: 7 residues within 4Å:- Chain B: E.386
- Chain O: A.33, L.102, Y.103, K.104
- Chain P: P.50, S.51
Ligand excluded by PLIPGOL.122: 8 residues within 4Å:- Chain P: N.13, S.14, E.15, P.64, P.65, N.68, E.70, G.71
Ligand excluded by PLIPGOL.123: 5 residues within 4Å:- Chain A: L.341
- Chain O: K.104
- Chain P: G.133, K.134, Y.137
Ligand excluded by PLIPGOL.124: 4 residues within 4Å:- Chain P: K.24, Q.25, E.28, K.110
Ligand excluded by PLIPGOL.125: 5 residues within 4Å:- Chain P: P.11, N.13, S.14, D.67, N.68
Ligand excluded by PLIP- 9 x UNL: UNKNOWN LIGAND
UNL.15: 4 residues within 4Å:- Chain A: R.16, F.17, W.20
- Ligands: UNL.102
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:W.20, A:W.20
- Hydrogen bonds: A:R.16
- Salt bridges: A:R.16
UNL.51: 7 residues within 4Å:- Chain B: W.90, F.161
- Ligands: CLA.24, CLA.25, CLA.26, CLA.36, BCR.39
No protein-ligand interaction detected (PLIP)UNL.80: 8 residues within 4Å:- Chain A: L.200, W.278
- Chain C: W.17
- Chain J: F.28, F.36
- Ligands: SQD.11, DGD.73, BCR.126
9 PLIP interactions:2 interactions with chain A, 4 interactions with chain J, 2 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: A:L.200, A:W.278, J:F.28, J:F.36, J:F.36, C:W.17, C:W.17
- Water bridges: J:F.36, D:R.223
UNL.92: 7 residues within 4Å:- Chain D: W.22, F.120, E.121
- Chain G: L.38
- Chain R: L.20
- Ligands: CLA.28, UNL.93
3 PLIP interactions:1 interactions with chain R, 1 interactions with chain G, 1 interactions with chain D- Hydrophobic interactions: R:L.20, G:L.38, D:E.121
UNL.93: 10 residues within 4Å:- Chain B: A.227
- Chain D: D.9, K.13, W.22
- Chain G: L.38
- Chain R: F.24
- Ligands: CLA.28, CLA.29, LMT.82, UNL.92
8 PLIP interactions:4 interactions with chain D, 3 interactions with chain R, 1 interactions with chain G- Hydrophobic interactions: D:W.22, D:W.22, R:F.24, R:F.24, R:F.24, G:L.38
- Hydrogen bonds: D:K.13
- Salt bridges: D:K.13
UNL.102: 8 residues within 4Å:- Chain A: A.100
- Chain H: M.1, E.2, T.3, L.4
- Ligands: BCR.10, UNL.15, SQD.16
4 PLIP interactions:4 interactions with chain H- Hydrophobic interactions: H:L.4
- Hydrogen bonds: H:E.2, H:T.3, H:T.3
UNL.106: 5 residues within 4Å:- Chain I: G.25, Y.29, Y.32
- Ligands: DGD.72, LMG.74
1 PLIP interactions:1 interactions with chain I- Hydrophobic interactions: I:Y.32
UNL.111: 2 residues within 4Å:- Chain L: I.23
- Ligands: LMT.110
1 PLIP interactions:1 interactions with chain L- Hydrophobic interactions: L:I.23
UNL.127: 5 residues within 4Å:- Chain D: W.83
- Chain R: S.15, G.16, V.19
- Ligands: CLA.84
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain R- Hydrophobic interactions: D:W.83, R:V.19
- 7 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.17: 6 residues within 4Å:- Chain A: I.50, I.53, L.72, Y.73
- Chain D: R.294
- Ligands: HTG.114
8 PLIP interactions:5 interactions with chain A, 1 interactions with chain M, 2 interactions with chain D- Hydrophobic interactions: A:I.50, A:I.53, A:L.72
- Hydrogen bonds: A:Y.73, D:R.294, D:R.294
- Water bridges: A:L.72, M:G.110
LMT.53: 4 residues within 4Å:- Chain B: Y.39, A.42, T.43
- Ligands: GOL.54
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:A.42
LMT.82: 16 residues within 4Å:- Chain B: R.223, L.224, A.227, K.497, D.500
- Chain D: E.1, R.2, F.5, D.6, D.9, D.10
- Chain G: W.24, M.30, M.34
- Chain R: R.38
- Ligands: UNL.93
15 PLIP interactions:7 interactions with chain B, 5 interactions with chain D, 1 interactions with chain R, 2 interactions with chain G- Hydrophobic interactions: B:A.227, G:W.24, G:W.24
- Hydrogen bonds: B:R.223, B:K.497, B:D.500, D:R.2, D:R.2, R:R.38
- Water bridges: B:K.497, D:E.1, D:E.1, D:D.9
- Salt bridges: B:R.223, B:K.497
LMT.95: 6 residues within 4Å:- Chain E: W.35, S.39
- Chain F: F.41, I.42, Q.43
- Chain I: I.23
5 PLIP interactions:3 interactions with chain F, 1 interactions with chain I, 1 interactions with chain E- Hydrophobic interactions: F:F.41, I:I.23
- Hydrogen bonds: F:Q.43, F:Q.43
- Water bridges: E:S.39
LMT.103: 11 residues within 4Å:- Chain A: W.14, E.15
- Chain C: W.241, R.244
- Chain H: V.20, F.21, L.24, S.25, G.26, R.30
- Ligands: CLA.61
10 PLIP interactions:5 interactions with chain H, 5 interactions with chain C- Hydrophobic interactions: H:V.20, H:F.21, H:L.24, C:W.241, C:W.241, C:W.241
- Hydrogen bonds: H:R.30, C:R.244, C:R.244
- Water bridges: H:R.30
LMT.109: 7 residues within 4Å:- Chain B: Y.39
- Chain L: N.4, Q.5, L.6
- Ligands: CLA.34, LMG.40, GOL.54
5 PLIP interactions:4 interactions with chain L, 1 interactions with chain B- Hydrophobic interactions: L:L.6
- Hydrogen bonds: L:Q.5
- Water bridges: L:N.4, L:Q.5, B:K.331
LMT.110: 7 residues within 4Å:- Chain L: V.27, E.30, S.31, Q.32, Q.33, K.34
- Ligands: UNL.111
4 PLIP interactions:4 interactions with chain L- Hydrogen bonds: L:E.30, L:Q.32, L:K.34, L:K.34
- 1 x OEX: CA-MN4-O5 CLUSTER(Covalent)
OEX.18: 10 residues within 4Å:- Chain A: D.170, V.185, E.189, H.332, E.333, H.337, D.342, A.344
- Chain C: E.336, R.339
18 PLIP interactions:10 interactions with chain A, 4 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, H2O.3, H2O.3, H2O.5, 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)
PL9.19: 26 residues within 4Å:- Chain A: F.211, M.214, H.215, L.218, H.252, F.255, A.263, S.264, F.265, L.271, F.274
- Chain D: F.28, P.29, A.31, Y.32, L.35
- Chain F: T.24, L.25
- Chain R: T.23, L.27
- Ligands: CLA.6, PHO.8, CLA.83, CLA.84, LHG.94, SQD.97
17 PLIP interactions:4 interactions with chain D, 10 interactions with chain A, 2 interactions with chain R, 1 interactions with chain F- Hydrophobic interactions: D:P.29, D:A.31, D:Y.32, D:L.35, A:F.211, A:L.218, A:F.255, A:F.255, A:F.265, A:L.271, A:L.271, A:F.274, R:T.23, R:L.27, F:L.25
- Hydrogen bonds: A:H.215, A:F.265
PL9.86: 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, L.200, I.203, H.204, T.207, 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.29, L.30
- Chain N: F.10
- Ligands: CLA.27, CLA.81, LHG.89, LHG.108
31 PLIP interactions:18 interactions with chain D, 5 interactions with chain K, 3 interactions with chain N, 5 interactions with chain A- Hydrophobic interactions: D:M.188, D:M.189, D:A.192, D:L.199, D:L.200, D:I.203, D:T.207, D:A.239, D:W.243, D:F.251, D:F.251, D:L.257, D:F.260, D:F.263, D:V.264, K:L.23, K:V.26, K:L.29, K:L.30, K:L.30, N:F.10, N:F.10, N:F.10, A:F.52, A:F.52, A:I.53, A:I.77, A:I.176
- Hydrogen bonds: D:H.204, D:F.251
- pi-Stacking: D:F.251
- 3 x CA: CALCIUM ION(Non-covalent)
CA.20: 1 residues within 4Å:- Chain B: N.437
No protein-ligand interaction detected (PLIP)CA.98: 2 residues within 4Å:- Chain F: R.44
- Ligands: GOL.99
5 PLIP interactions:1 interactions with chain F, 4 Ligand-Water interactions- Metal complexes: F:R.44, H2O.32, H2O.32, H2O.32, H2O.46
CA.112: 3 residues within 4Å:- Chain M: T.136, N.198, V.199
5 PLIP interactions:2 interactions with chain M, 3 Ligand-Water interactions- Metal complexes: M:T.136, M:V.199, H2O.36, H2O.37, H2O.40
- 6 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
LMG.40: 21 residues within 4Å:- Chain B: Y.39, T.326, G.327, P.328, K.331, A.453, F.457
- Chain D: I.274
- Chain K: F.35
- Chain L: N.4, L.6, A.10, L.13
- Ligands: CLA.27, CLA.33, CLA.34, BCR.37, BCR.38, GOL.54, LHG.108, LMT.109
16 PLIP interactions:5 interactions with chain L, 8 interactions with chain B, 2 interactions with chain K, 1 interactions with chain D- Hydrophobic interactions: L:A.10, L:L.13, B:A.453, B:F.457, K:F.35, K:F.35, D:I.274
- Hydrogen bonds: L:N.4, B:Y.39, B:T.326, B:T.326
- Water bridges: L:N.4, L:N.4, B:T.326, B:T.326, B:K.331
LMG.55: 19 residues within 4Å:- Chain A: F.93, W.97, E.98, F.117, L.121
- Chain C: L.195, L.196, K.197, S.198, F.200, E.203, W.205, M.263, F.266
- Chain H: K.5, Y.9
- Ligands: CLA.9, CLA.60, DGD.71
13 PLIP interactions:5 interactions with chain A, 5 interactions with chain C, 3 interactions with chain H- Hydrophobic interactions: A:F.93, A:F.117, A:L.121, C:W.205, C:F.266
- Hydrogen bonds: A:W.97, A:E.98, C:E.203, H:K.5, H:K.5, H:Y.9
- Water bridges: C:S.198, C:S.198
LMG.74: 11 residues within 4Å:- Chain C: F.52, H.56, Q.66
- Chain J: D.14, V.18
- Chain Q: Q.5, I.9
- Ligands: CLA.59, CLA.63, DGD.72, UNL.106
6 PLIP interactions:2 interactions with chain Q, 1 interactions with chain J, 3 interactions with chain C- Hydrophobic interactions: Q:I.9, J:V.18
- Water bridges: Q:Q.5, C:H.56
- Hydrogen bonds: C:H.56
- Salt bridges: C:H.56
LMG.75: 13 residues within 4Å:- Chain C: W.79, D.89, F.91, P.92, V.95, V.99, H.100, S.103
- Chain S: F.59, V.62
- Ligands: CLA.58, BCR.69, HTG.76
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain S- Hydrophobic interactions: C:W.79, C:P.92, C:V.99, C:V.99
- Hydrogen bonds: S:V.62, S:V.62
LMG.104: 20 residues within 4Å:- Chain D: L.35, 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.6, DGD.73, CLA.83, BCR.85, MG.105
12 PLIP interactions:7 interactions with chain D, 3 interactions with chain I, 2 interactions with chain F- Hydrophobic interactions: D:L.35, D:L.39, D:F.63, D:F.63, D:F.63
- Hydrogen bonds: D:F.63, I:G.30, F:M.39, F:Q.40
- Water bridges: D:N.62, I:F.27, I:G.36
LMG.128: 11 residues within 4Å:- Chain C: A.105, F.109, Y.113, R.117
- Chain S: Y.27, W.33, K.37, F.41, W.47
- Ligands: CLA.68, BCR.107
13 PLIP interactions:7 interactions with chain C, 6 interactions with chain S- Hydrophobic interactions: C:A.105, C:F.109, C:F.109, C:F.109, C:F.109, S:F.41, S:W.47, S:W.47
- Hydrogen bonds: C:Y.113, C:R.117, S:W.33
- Salt bridges: S:K.37, S:K.37
- 10 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
HTG.41: 7 residues within 4Å:- Chain B: L.41, S.73, S.75, W.77, E.93, L.97
- Ligands: GOL.52
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:L.97
- Hydrogen bonds: B:S.73, B:S.75, B:E.93
- Water bridges: B:W.77
HTG.42: 11 residues within 4Å:- Chain B: K.340, S.418, Y.419, K.422, E.430, F.431
- Chain M: Q.174, A.175, K.176, E.177, E.178
8 PLIP interactions:6 interactions with chain B, 2 interactions with chain M- Hydrogen bonds: B:K.340, B:K.340, B:K.422, B:E.430, B:F.431, B:F.431, M:Q.174, M:K.176
HTG.43: 3 residues within 4Å:- Chain B: W.184, A.203
- Ligands: CLA.21
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:W.184, B:A.203
HTG.49: 7 residues within 4Å:- Chain B: W.74, D.86, G.88, F.89, L.97
- Ligands: HTG.50, GOL.52
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:W.74, B:L.97
- Hydrogen bonds: B:D.86, B:G.88, B:G.88
HTG.50: 4 residues within 4Å:- Chain B: D.86, G.88, F.89
- Ligands: HTG.49
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:F.89
- Water bridges: B:W.90
HTG.76: 5 residues within 4Å:- Chain C: W.79, F.164, G.165
- Ligands: CLA.57, LMG.75
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:W.79
HTG.77: 7 residues within 4Å:- Chain C: V.158, M.162, T.182, N.183, P.184, L.186, I.220
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:V.158, C:I.220
- Hydrogen bonds: C:N.183, C:P.184
HTG.91: 6 residues within 4Å:- Chain D: G.3, W.4, F.5
- Chain G: W.24, T.27, P.28
7 PLIP interactions:3 interactions with chain D, 4 interactions with chain G- Hydrogen bonds: D:W.4, D:F.5
- Water bridges: D:G.3, G:W.24
- Hydrophobic interactions: G:W.24, G:W.24, G:T.27
HTG.114: 6 residues within 4Å:- Chain A: Y.73
- Chain M: G.110, G.111
- Ligands: BCR.10, GOL.12, LMT.17
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain M- Water bridges: A:D.103, A:D.103, M:G.110
HTG.121: 6 residues within 4Å:- Chain P: A.89, E.90, R.96, S.97, D.99, I.100
2 PLIP interactions:2 interactions with chain P- Hydrogen bonds: P:R.96, P:D.99
- 5 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
DGD.71: 30 residues within 4Å:- Chain A: L.91, S.148, L.151, F.155, 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, C.270, F.274, N.275, N.276, T.277, D.342, F.343, R.344, L.420
- Ligands: CLA.9, LMG.55, CLA.60, CLA.61
20 PLIP interactions:4 interactions with chain A, 16 interactions with chain C- Hydrophobic interactions: A:L.151, A:F.155, A:I.160, A:I.163, C:P.199, C:F.200, C:F.200, C:W.205, C:V.207
- Hydrogen bonds: C:G.202, C:N.276, C:T.277, C:T.277, C:D.342, C:D.342, C:R.344, C:R.344
- Water bridges: C:F.200, C:D.342, C:D.342
DGD.72: 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: F.28, Y.32
- Ligands: CLA.59, DGD.73, LMG.74, UNL.106
16 PLIP interactions:12 interactions with chain C, 2 interactions with chain I, 2 interactions with chain A- Hydrophobic interactions: C:L.386, I:F.28, A:F.197, A:F.197
- Hydrogen bonds: C:S.388, C:N.400, C:N.400, C:V.402, C:V.402, C:W.407
- Water bridges: C:K.61, C:E.65, C:Q.66, C:G.67, C:G.67, I:Y.32
DGD.73: 29 residues within 4Å:- Chain A: P.196, Q.199, L.200, A.203, 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: L.64
- Chain I: F.28, A.31, Y.32, G.36, S.37, S.38
- Chain P: Q.34
- Ligands: CLA.6, CLA.59, DGD.72, UNL.80, LHG.90, LMG.104
19 PLIP interactions:6 interactions with chain C, 3 interactions with chain I, 7 interactions with chain A, 1 interactions with chain D, 2 interactions with chain P- Hydrogen bonds: C:N.387, C:N.397, C:S.398, C:V.399, I:G.36, A:S.305, P:Q.34, P:Q.34
- Water bridges: C:N.397, C:N.400, I:Y.32, I:S.38
- Hydrophobic interactions: A:P.196, A:Q.199, A:L.200, A:A.203, A:F.300, A:F.300, D:L.64
DGD.87: 11 residues within 4Å:- Chain D: G.89, F.91, T.92
- Chain E: F.37, D.45, V.46, F.47, R.51
- Chain T: D.1
- Ligands: BCR.85, SQD.97
11 PLIP interactions:6 interactions with chain D, 4 interactions with chain E, 1 interactions with chain T- Hydrophobic interactions: D:F.91, D:F.91, D:F.91, D:F.91, E:F.37, E:F.37, E:F.47
- Hydrogen bonds: D:T.92, D:T.92, E:R.51, T:D.1
DGD.101: 25 residues within 4Å:- Chain B: Y.192, F.249, Y.257, Y.272, Q.273, S.276, Y.278, F.462
- Chain D: G.76, H.77, F.110, I.113, V.144, I.149, L.152, G.153, L.281
- Chain G: L.45, Y.48, N.49, V.59, S.60, W.61
- Ligands: CLA.22, CLA.28
23 PLIP interactions:7 interactions with chain B, 8 interactions with chain G, 8 interactions with chain D- Hydrophobic interactions: B:F.249, B:Y.257, B:F.462, B:F.462, G:L.45, G:Y.48, G:Y.48, G:Y.48, D:F.110, D:V.144, D:I.149, D:L.152, D:L.152, D:L.281
- Hydrogen bonds: B:Y.192, B:Y.192, B:Q.273, G:N.49, G:V.59, G:S.60, G:W.61, D:H.77, D:S.155
- 5 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
LHG.88: 21 residues within 4Å:- Chain A: S.232, N.234
- Chain B: W.4, Y.5, R.6, L.460, F.463, W.467
- Chain D: Y.131, I.134, W.256, F.259, F.263, T.267, M.271
- Chain K: L.23
- Chain L: P.18
- Ligands: CLA.27, CLA.31, CLA.33, LHG.108
16 PLIP interactions:10 interactions with chain B, 4 interactions with chain D, 2 interactions with chain A- Hydrophobic interactions: B:W.4, B:W.4, B:L.460, B:F.463, B:F.463, D:F.263
- Water bridges: B:R.6, B:R.6, B:R.6, B:R.6, D:R.129, D:R.129
- Salt bridges: B:R.6
- Hydrogen bonds: D:Y.131, A:S.232, A:N.234
LHG.89: 26 residues within 4Å:- Chain A: M.37, R.129
- 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
- Ligands: PHO.7, CLA.81, PL9.86, LHG.108, GOL.115, BCR.116
17 PLIP interactions:7 interactions with chain K, 4 interactions with chain N, 6 interactions with chain D- Hydrophobic interactions: K:Y.18, K:L.22, K:L.29, N:F.17, N:F.17, N:F.17, N:A.20, D:F.251, D:F.251, D:F.260
- Hydrogen bonds: K:N.13, K:N.13, K:T.15, K:S.16, D:S.252, D:S.252, D:N.253
LHG.90: 21 residues within 4Å:- Chain A: R.140, W.142, L.200, F.273, A.276, V.281
- Chain C: F.15, W.18, W.425, R.429
- Chain D: E.209, N.210, A.219, S.220, T.221, F.222
- Ligands: SQD.11, CLA.59, CLA.63, CLA.65, DGD.73
15 PLIP interactions:4 interactions with chain C, 5 interactions with chain D, 6 interactions with chain A- Hydrophobic interactions: C:W.18, C:W.18, A:W.142, A:L.200, A:F.273, A:A.276, A:V.281
- Hydrogen bonds: C:R.429, C:R.429, D:N.210, D:A.219, D:S.220, D:T.221
- Water bridges: D:T.221
- Salt bridges: A:R.140
LHG.94: 15 residues within 4Å:- Chain A: L.258, F.260, Y.262
- Chain D: F.17, V.18
- Chain E: T.4, T.5, E.7, P.9, F.10, S.11
- Chain F: R.18, A.21
- Ligands: CLA.6, PL9.19
13 PLIP interactions:10 interactions with chain E, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain F- Hydrophobic interactions: E:F.10, D:V.18, A:F.260, F:A.21
- Hydrogen bonds: E:T.4, E:T.5, E:T.5, E:T.5, E:E.7, E:E.7, E:E.7, E:F.10, E:S.11
LHG.108: 26 residues within 4Å:- Chain A: S.232, N.234
- Chain B: P.3, W.4, Y.5
- Chain D: W.256, F.260, F.263
- Chain K: E.11, L.12, N.13, S.16, L.19, G.20, L.22, L.23, V.26
- Chain L: V.17, F.21
- Ligands: CLA.31, CLA.34, LMG.40, CLA.81, PL9.86, LHG.88, LHG.89
14 PLIP interactions:6 interactions with chain K, 1 interactions with chain D, 2 interactions with chain L, 2 interactions with chain B, 3 interactions with chain A- Hydrophobic interactions: K:L.22, K:V.26, K:V.26, D:F.260, L:V.17, L:F.21
- Hydrogen bonds: K:E.11, K:N.13, K:S.16, B:W.4, B:Y.5, A:S.232, A:S.232, A:N.234
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.96: 19 residues within 4Å:- Chain E: F.10, I.13, R.18, Y.19, I.22, H.23, T.26, I.27, L.30
- Chain F: I.14, R.18, W.19, V.22, H.23, A.26, V.27, I.30
- Chain T: A.18, I.22
20 PLIP interactions:10 interactions with chain F, 8 interactions with chain E, 2 interactions with chain T,- Hydrophobic interactions: F:I.14, F:W.19, F:V.22, F:A.26, F:V.27, E:F.10, E:I.13, E:T.26, E:I.27, E:I.27, T:A.18, T:I.22
- Salt bridges: F:R.18, E:R.18
- pi-Stacking: F:W.19, F:W.19, E:Y.19
- pi-Cation interactions: F:H.23
- Metal complexes: F:H.23, E:H.23
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x HEC: HEME C(Covalent)
HEC.120: 24 residues within 4Å:- Chain P: A.36, C.37, S.39, C.40, H.41, T.46, T.48, L.52, D.53, L.54, T.58, L.59, A.62, L.72, Y.75, M.76, T.81, Y.82, I.88, H.92, P.93, I.115, I.119
- Ligands: GOL.78
16 PLIP interactions:16 interactions with chain P,- Hydrophobic interactions: P:A.36, P:T.46, 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:Y.82
- 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., Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses. Nature (2015)
- Release Date
- 2014-12-03
- Peptides
- Photosystem Q(B) protein: A
Photosystem II CP47 chlorophyll apoprotein: B
Photosystem II 44 kDa 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: M
Photosystem II reaction center protein T: N
Photosystem II 12 kDa extrinsic protein: O
Cytochrome c-550: P
Photosystem II reaction center protein Ycf12: Q
Photosystem II reaction center protein X: R
Photosystem II reaction center protein Z: S
Photosystem II protein Y: T - 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
YR
XS
ZT
R - Membrane
-
We predict this structure to be a membrane protein.
SMTL ID : 4ub8.1 (1 other biounit)
Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser
Photosystem Q(B) protein
Photosystem II CP47 chlorophyll apoprotein
Photosystem II 44 kDa 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 J
Photosystem II reaction center protein K
Photosystem II reaction center protein L
Photosystem II reaction center 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 Ycf12
Photosystem II reaction center protein X
Photosystem II reaction center protein Z
Photosystem II protein Y
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