- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-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.7: 25 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, I.203, W.243, F.247
- Ligands: CLA.4, CLA.5
19 PLIP interactions:16 interactions with chain A, 3 interactions with chain D- Hydrophobic interactions: A:L.41, A:A.44, A:F.48, A:I.115, A:F.119, A:F.119, A:Y.126, A:A.146, A:Y.147, A:Y.147, A:P.150, A:F.158, A:V.205, A:P.279, D:L.195, D:A.198, D:L.199
- Hydrogen bonds: A:Y.126, A:Q.130
PHO.8: 32 residues within 4Å:- Chain A: F.206, A.209, L.210, A.213, M.214, F.255, L.258, I.259
- Chain D: L.27, A.31, L.35, W.38, I.104, G.108, G.111, L.112, F.115, Q.119, N.132, A.135, F.136, P.139, F.143, F.163, G.164, V.165, P.265, V.266, L.269
- Ligands: CLA.6, PL9.16, CLA.75
21 PLIP interactions:18 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: D:A.31, D:L.35, D:W.38, D:W.38, D:W.38, D:I.104, D:L.112, D:F.115, 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: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: 17 residues within 4Å:- Chain A: F.17, 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
- Ligands: CLA.9, UNL.17, UNL.92
9 PLIP interactions:1 interactions with chain H, 8 interactions with chain A- Hydrophobic interactions: H:F.15, A:F.17, A:P.39, A:I.46, A:I.50, A:A.51, A:I.96, A:W.105, A:L.106
BCR.37: 12 residues within 4Å:- Chain B: M.24, L.28, C.111, W.114
- Chain L: L.13
- Ligands: CLA.27, CLA.33, CLA.34, BCR.38, SQD.40, LMG.41, LHG.98
6 PLIP interactions:1 interactions with chain L, 5 interactions with chain B- Hydrophobic interactions: L:L.13, B:L.28, B:L.28, B:W.114, B:W.114, B:W.114
BCR.38: 14 residues within 4Å:- Chain B: L.28, G.31, W.32, S.35, I.100, V.101, S.103, G.104
- Ligands: CLA.24, CLA.27, CLA.33, BCR.37, SQD.40, LMG.41
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:L.28, B:W.32
BCR.39: 12 residues within 4Å:- Chain B: L.102, L.105, L.108, A.109, C.111, W.112, V.115
- Ligands: CLA.25, CLA.26, CLA.35, CLA.36, UNL.49
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.102, B:W.112, B:V.115
BCR.64: 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.62, CLA.63, LMG.70
11 PLIP interactions:8 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:V.106, C:L.107, C:F.129, S:V.51, S:N.58, S:F.59
BCR.65: 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: V.20, F.23, L.24
- Ligands: CLA.51, CLA.55, CLA.56, CLA.57
12 PLIP interactions:2 interactions with chain H, 10 interactions with chain C- Hydrophobic interactions: H:F.23, H:L.24, C:I.191, C:F.192, C:Y.194, C:L.195, C:L.195, C:I.206, C:V.209, C:I.222, C:I.222, C:F.246
BCR.77: 16 residues within 4Å:- Chain D: Y.32, L.33, G.36, G.37, L.39, T.40, F.91
- Chain F: P.28, T.29, F.32, L.33, I.36
- Chain I: V.20, V.24
- Ligands: DGD.67, LMG.93
13 PLIP interactions:2 interactions with chain I, 7 interactions with chain F, 4 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:F.32, F:L.33, F:I.36, D:Y.32, D:L.33, D:L.39, D:F.91
BCR.89: 17 residues within 4Å:- Chain G: M.30, 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.21, CLA.22, CLA.23, CLA.29, CLA.30
11 PLIP interactions:9 interactions with chain G, 2 interactions with chain Q- Hydrophobic interactions: G:L.36, G:F.37, G:F.37, G:F.37, G:F.37, G:V.39, G:F.40, G:I.43, G:L.54, Q:L.6, Q:F.10
BCR.97: 18 residues within 4Å:- Chain C: A.37, G.40, L.41, L.101, S.104, A.105, G.108, A.115
- Chain J: Y.6, F.9, L.16, F.23, W.30
- Chain S: L.9, L.12, S.16
- Ligands: CLA.61, BCR.109
13 PLIP interactions:5 interactions with chain C, 6 interactions with chain J, 2 interactions with chain S- Hydrophobic interactions: C:A.37, C:L.41, C:L.101, C:A.105, C:A.115, J:Y.6, J:F.9, J:L.16, J:F.23, J:F.23, J:W.30, S:L.9, S:L.12
BCR.103: 11 residues within 4Å:- Chain A: L.28
- Chain N: I.4, F.8, A.11, I.14, A.15, F.17, F.18, I.21, F.22
- Ligands: SQD.13
11 PLIP interactions:10 interactions with chain N, 1 interactions with chain A- Hydrophobic interactions: N:I.4, N:F.8, N:A.11, N:I.14, N:F.17, N:F.18, N:F.18, N:I.21, N:F.22, N:F.22, A:L.28
BCR.109: 22 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, F.23, A.25, V.29
- Chain R: I.12, G.13, G.16, P.17
- Chain S: V.13, S.16, F.17
- Ligands: SQD.11, UNL.96, BCR.97
13 PLIP interactions:8 interactions with chain J, 3 interactions with chain R, 1 interactions with chain S, 1 interactions with chain C- Hydrophobic interactions: J:L.12, J:L.16, J:I.19, J:I.19, J:L.22, J:F.23, J:A.25, J:V.29, R:I.12, R:I.12, R:P.17, S:F.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: 24 residues within 4Å:- Chain A: L.200, A.203, G.204, N.267, S.270, F.273, F.274, A.277, W.278, V.281
- Chain C: Q.10, A.16, W.18
- Chain D: S.220, F.222, R.223
- Chain I: I.21
- Chain J: A.25, F.28
- Ligands: CLA.58, LMG.69, LHG.80, UNL.96, BCR.109
18 PLIP interactions:11 interactions with chain A, 2 interactions with chain C, 1 interactions with chain I, 2 interactions with chain J, 2 interactions with chain D- Hydrophobic interactions: A:A.203, A:F.273, A:F.274, A:A.277, A:W.278, A:W.278, A:V.281, C:W.18, I:I.21, J:A.25, J:F.28
- Hydrogen bonds: A:N.267, A:S.270, C:Q.10, D:S.220, D:S.220
- Water bridges: A:N.266, A:N.267
SQD.13: 13 residues within 4Å:- Chain A: W.20, N.26, R.27, L.28, V.30, L.42, T.45
- Chain N: F.22
- Ligands: CLA.5, UNL.17, LHG.79, UNL.92, BCR.103
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:N.26, A:L.28, A:V.30, A:L.42, A:T.45
- Hydrogen bonds: A:N.26, A:R.27, A:L.28
SQD.40: 8 residues within 4Å:- Chain B: R.17, L.28, S.103, W.114
- Chain K: R.7
- Ligands: CLA.34, BCR.37, BCR.38
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain K- Hydrophobic interactions: B:L.28
- Salt bridges: B:R.17, K:R.7
SQD.88: 13 residues within 4Å:- Chain D: R.14, R.16
- Chain E: E.7
- Chain F: F.15, T.16, V.17, V.20
- Chain Q: T.23, I.30, D.34
- Chain T: Q.29, L.33
- Ligands: PL9.16
11 PLIP interactions:2 interactions with chain Q, 3 interactions with chain D, 4 interactions with chain F, 1 interactions with chain T, 1 interactions with chain E- Hydrophobic interactions: Q:I.30, F:V.17, F:V.20
- Hydrogen bonds: Q:D.34, D:R.14, F:V.17, T:Q.29, E:E.7
- Salt bridges: D:R.14, D:R.16
- Water bridges: F:R.18
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.12: 1 residues within 4Å:- Chain A: D.103
3 PLIP interactions:3 interactions with chain A- Water bridges: A:D.103, A:D.103, A:D.103
GOL.46: 8 residues within 4Å:- Chain B: W.274, D.275, S.277, R.356, R.357, M.358, P.359
- Chain D: E.327
6 PLIP interactions:1 interactions with chain D, 5 interactions with chain B- Hydrogen bonds: D:E.327, B:W.274, B:S.277, B:R.356, B:R.356
- Water bridges: B:S.277
GOL.47: 7 residues within 4Å:- Chain B: P.49, P.53, M.54, I.79, W.166, E.265, K.307
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:M.54, B:K.307, B:K.307
- Water bridges: B:E.265, B:K.307
GOL.74: 9 residues within 4Å:- Chain A: L.341
- Chain C: M.378, T.379, H.380, A.381, G.391, V.392, E.395
- Chain P: K.47
8 PLIP interactions:4 interactions with chain C, 4 interactions with chain P- Hydrogen bonds: C:M.378, C:A.381, C:V.392, P:K.47
- Water bridges: C:T.379, P:S.39, P:K.47, P:K.47
GOL.105: 6 residues within 4Å:- Chain C: E.395
- Chain O: K.104
- Chain P: I.45, G.133, K.134, Y.137
7 PLIP interactions:3 interactions with chain O, 1 interactions with chain C, 3 interactions with chain P- Water bridges: O:K.104, O:K.104, O:K.104, P:K.134, P:K.134
- Hydrogen bonds: C:E.395, P:K.134
- 1 x OEX: CA-MN4-O5 CLUSTER(Covalent)
OEX.14: 10 residues within 4Å:- Chain A: D.170, E.189, H.332, E.333, H.337, D.342, A.344
- Chain C: E.336, R.339
- Ligands: OEY.15
17 PLIP interactions:9 interactions with chain A, 4 interactions with chain C, 4 Ligand-Water interactions- 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.1, H2O.2, H2O.3, H2O.5
- Hydrogen bonds: C:R.339, C:R.339
- 1 x OEY: CA-MN4-O6 CLUSTER(Covalent)
OEY.15: 11 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
- Ligands: OEX.14
18 PLIP interactions:10 interactions with chain A, 4 interactions with chain C, 4 Ligand-Water interactions- Metal complexes: A:D.170, A:D.170, A:E.189, 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.1, H2O.2, H2O.3, 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: 31 residues within 4Å:- Chain A: F.211, M.214, H.215, L.218, V.219, Y.246, I.248, A.251, H.252, F.255, A.263, S.264, F.265, L.271, F.274, L.275
- Chain D: F.28, P.29, A.31, L.35
- Chain F: A.21, T.24, L.25
- Chain Q: T.23, L.27
- Ligands: CLA.6, PHO.8, CLA.75, CLA.76, LHG.85, SQD.88
22 PLIP interactions:16 interactions with chain A, 3 interactions with chain D, 2 interactions with chain Q, 1 interactions with chain F- Hydrophobic interactions: A:F.211, A:M.214, A:L.218, A:V.219, A:Y.246, A:I.248, A:A.251, A:F.255, A:F.255, A:F.255, A:L.271, A:L.271, A:F.274, A:L.275, D:F.28, D:A.31, D:L.35, Q:T.23, Q:L.27, F:L.25
- Hydrogen bonds: A:H.215, A:F.265
PL9.78: 33 residues within 4Å:- Chain A: V.49, F.52, I.53, I.77, I.176
- Chain D: M.188, M.189, A.192, G.193, L.199, L.200, 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.29
- Chain N: F.10
- Ligands: CLA.5, LHG.79, LHG.98
26 PLIP interactions:15 interactions with chain D, 5 interactions with chain A, 4 interactions with chain N, 2 interactions with chain K- Hydrophobic interactions: D:M.189, D:L.199, D:L.200, D:T.207, D:Y.234, D:W.243, D:F.251, D:F.251, D:F.251, D:L.257, D:F.260, D:F.263, D:V.264, A:V.49, 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.29
- Hydrogen bonds: D:H.204, D:F.251
- 9 x UNL: UNKNOWN LIGAND
UNL.17: 8 residues within 4Å:- Chain A: L.13, R.16, F.17, W.20
- Ligands: CLA.9, BCR.10, SQD.13, UNL.92
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:L.13, A:F.17, A:W.20
- Salt bridges: A:R.16
UNL.49: 6 residues within 4Å:- Chain B: W.90
- Ligands: CLA.24, CLA.25, CLA.26, CLA.36, BCR.39
No protein-ligand interaction detected (PLIP)UNL.81: 8 residues within 4Å:- Chain D: W.22, S.23, F.120, E.121
- Chain G: L.38
- Chain Q: L.20
- Ligands: UNL.82, UNL.108
4 PLIP interactions:2 interactions with chain D, 1 interactions with chain G, 1 interactions with chain Q- Hydrophobic interactions: D:W.22, D:E.121, G:L.38, Q:L.20
UNL.82: 10 residues within 4Å:- Chain B: A.227
- Chain D: F.5, K.13, W.22, R.124
- Chain Q: F.24
- Ligands: CLA.28, CLA.29, LMT.42, UNL.81
7 PLIP interactions:5 interactions with chain D, 2 interactions with chain Q- Hydrophobic interactions: D:F.5, D:W.22, D:W.22, Q:F.24, Q:F.24
- Hydrogen bonds: D:K.13
- Salt bridges: D:K.13
UNL.92: 7 residues within 4Å:- Chain H: M.1, T.3, L.4, T.7
- Ligands: BCR.10, SQD.13, UNL.17
4 PLIP interactions:4 interactions with chain H- Hydrophobic interactions: H:T.3, H:L.4, H:T.7
- Hydrogen bonds: H:T.3
UNL.94: 6 residues within 4Å:- Chain I: G.25, F.28, Y.29, Y.32
- Ligands: DGD.67, LMG.69
2 PLIP interactions:2 interactions with chain I- Hydrophobic interactions: I:F.28, I:Y.32
UNL.96: 5 residues within 4Å:- Chain C: W.17
- Chain J: F.36
- Ligands: SQD.11, LHG.80, BCR.109
1 PLIP interactions:1 interactions with chain J- Hydrophobic interactions: J:F.36
UNL.100: 2 residues within 4Å:- Chain L: I.23
- Ligands: LMT.99
1 PLIP interactions:1 interactions with chain L- Hydrophobic interactions: L:I.23
UNL.108: 8 residues within 4Å:- Chain D: L.82, W.83, G.89
- Chain Q: S.15, G.16, L.20
- Ligands: CLA.76, UNL.81
3 PLIP interactions:1 interactions with chain Q, 2 interactions with chain D- Hydrophobic interactions: Q:L.20, D:L.82, D:W.83
- 6 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
LMG.18: 21 residues within 4Å:- Chain A: F.93, W.97, E.98, F.117, L.121, S.124, F.155
- Chain C: L.196, K.197, S.198, P.199, F.200, E.203, W.205, M.263, F.266
- Chain H: K.5, Y.9
- Ligands: CLA.9, CLA.55, DGD.66
16 PLIP interactions:7 interactions with chain C, 1 interactions with chain H, 8 interactions with chain A- Hydrophobic interactions: C:F.200, C:W.205, C:W.205, C:F.266, C:F.266, A:F.93, A:F.117, A:L.121, A:L.121, A:F.155, A:F.155
- Hydrogen bonds: C:S.198, C:E.203, H:Y.9, A:W.97, A:E.98
LMG.41: 19 residues within 4Å:- Chain B: Y.39, T.326, G.327, P.328, K.331
- Chain D: I.274
- Chain K: F.35
- Chain L: N.4, L.6, A.10, L.13, F.14, V.17
- Ligands: CLA.27, CLA.33, CLA.34, BCR.37, BCR.38, LHG.98
12 PLIP interactions:2 interactions with chain K, 4 interactions with chain L, 5 interactions with chain B, 1 interactions with chain D- Hydrophobic interactions: K:F.35, K:F.35, L:L.13, L:F.14, L:V.17, D:I.274
- Hydrogen bonds: L:N.4, B:Y.39, B:T.326, B:T.326
- Water bridges: B:K.331, B:K.331
LMG.69: 15 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, I.9
- Ligands: SQD.11, CLA.52, CLA.54, CLA.58, DGD.67, UNL.94
9 PLIP interactions:1 interactions with chain I, 3 interactions with chain J, 3 interactions with chain C, 2 interactions with chain R- Hydrophobic interactions: I:I.21, J:D.14, J:V.18, J:V.21, R:I.9
- Hydrogen bonds: C:H.56, R:Q.5
- Salt bridges: C:H.56, C:H.56
LMG.70: 14 residues within 4Å:- Chain C: V.43, W.79, D.89, F.91, V.95, V.99, H.100, S.103
- Chain S: F.59, V.62
- Ligands: CLA.53, CLA.63, BCR.64, HTG.71
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:V.43, C:W.79, C:W.79, C:V.95, C:V.99
LMG.93: 17 residues within 4Å:- Chain D: 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.68, BCR.77, MG.95
13 PLIP interactions:3 interactions with chain F, 6 interactions with chain D, 4 interactions with chain I- Hydrophobic interactions: F:T.29, D:F.63, D:F.63, D:F.63, D:F.63, I:F.27
- Hydrogen bonds: F:M.39, F:Q.40, D:F.63, I:G.30
- Water bridges: D:N.62, I:F.27, I:G.36
LMG.110: 11 residues within 4Å:- Chain C: F.109, Y.113, R.117
- Chain S: Y.27, W.33, K.37, I.40, F.41, W.47
- Ligands: CLA.61, CLA.63
10 PLIP interactions:5 interactions with chain S, 5 interactions with chain C- Hydrophobic interactions: S:I.40, S:F.41, 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, C:R.117
- 7 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.20: 4 residues within 4Å:- Chain A: L.72, Y.73
- Chain D: R.294
- Chain M: G.110
6 PLIP interactions:3 interactions with chain A, 2 interactions with chain D, 1 interactions with chain M- Hydrophobic interactions: A:L.72
- Hydrogen bonds: A:L.72, A:Y.73, D:R.294, D:R.294, M:G.110
LMT.42: 16 residues within 4Å:- Chain B: R.223, L.224, K.226, K.497, D.500
- Chain D: R.2, F.5, D.6, D.9, D.10
- Chain G: W.24, M.30, A.31, M.34
- Chain Q: R.38
- Ligands: UNL.82
11 PLIP interactions:5 interactions with chain B, 3 interactions with chain G, 1 interactions with chain Q, 2 interactions with chain D- Hydrophobic interactions: B:L.224, G:W.24, G:W.24, G:A.31
- Hydrogen bonds: B:K.497, B:D.500, Q:R.38, D:R.2, D:D.9
- Salt bridges: B:R.223, B:K.497
LMT.50: 2 residues within 4Å:- Chain B: S.35, A.42
No protein-ligand interaction detected (PLIP)LMT.86: 5 residues within 4Å:- Chain E: W.35, S.39
- Chain F: F.41, I.42, Q.43
5 PLIP interactions:3 interactions with chain F, 2 interactions with chain E- Hydrophobic interactions: F:F.41, E:W.35, E:W.35
- Hydrogen bonds: F:Q.43, F:Q.43
LMT.91: 9 residues within 4Å:- Chain A: W.14, E.15
- Chain C: W.241, R.244
- Chain H: L.24, S.25, G.26, R.30
- Ligands: CLA.56
5 PLIP interactions:3 interactions with chain C, 2 interactions with chain H- Hydrophobic interactions: C:W.241
- Hydrogen bonds: C:R.244, C:R.244, H:R.30
- Water bridges: H:R.30
LMT.99: 6 residues within 4Å:- Chain L: V.27, E.30, S.31, Q.32, Q.33
- Ligands: UNL.100
1 PLIP interactions:1 interactions with chain L- Hydrogen bonds: L:E.30
LMT.101: 6 residues within 4Å:- Chain L: M.1, E.2, Q.5, A.12
- Chain N: I.4, F.8
6 PLIP interactions:2 interactions with chain L, 4 interactions with chain N- Hydrophobic interactions: L:A.12, N:I.4, N:I.4, N:F.8, N:F.8
- Hydrogen bonds: L:Q.5
- 8 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
HTG.43: 6 residues within 4Å:- Chain B: S.73, W.74, S.75, W.77, E.93, L.97
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:W.74, B:L.97
- Hydrogen bonds: B:S.73, B:S.75, B:E.93
HTG.44: 12 residues within 4Å:- Chain B: K.340, S.418, Y.419, K.422, F.429, E.430, F.431, T.433
- Chain M: Q.174, A.175, K.176, E.177
10 PLIP interactions:4 interactions with chain M, 6 interactions with chain B- Hydrogen bonds: M:Q.174, M:K.176, B:K.340, B:K.340, B:K.422, B:E.430, B:F.431, B:F.431
- Water bridges: M:E.177, M:E.177
HTG.45: 3 residues within 4Å:- Chain B: W.184, I.206
- Ligands: CLA.21
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:W.184, B:W.184, B:I.206
HTG.48: 5 residues within 4Å:- Chain B: W.74, D.86, G.88, F.89, L.97
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.71: 5 residues within 4Å:- Chain C: W.79, F.164, G.165
- Ligands: CLA.52, LMG.70
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:W.79
HTG.72: 4 residues within 4Å:- Chain C: F.163, N.183, P.184, L.186
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.183
HTG.83: 5 residues within 4Å:- Chain D: G.3, W.4, F.5
- Chain G: W.24, P.28
2 PLIP interactions:1 interactions with chain G, 1 interactions with chain D- Hydrophobic interactions: G:W.24
- Hydrogen bonds: D:F.5
HTG.107: 6 residues within 4Å:- Chain P: A.89, E.90, R.96, S.97, D.99, I.100
3 PLIP interactions:3 interactions with chain P- Hydrogen bonds: P:E.90, P:R.96, P:D.99
- 4 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
DGD.66: 32 residues within 4Å:- Chain A: L.91, S.148, L.151, A.152, 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, F.266, C.270, F.274, N.275, N.276, T.277, D.342, F.343, R.344, L.420
- Ligands: CLA.9, LMG.18, CLA.55, CLA.56
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, C:F.266
- 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:P.199, C:F.200
DGD.67: 20 residues within 4Å:- Chain A: F.197, L.297
- Chain C: E.65, Q.66, G.67, L.386, S.388, N.400, F.401, V.402, W.407, T.410
- Chain I: F.28, Y.32
- Ligands: CLA.54, CLA.58, DGD.68, LMG.69, BCR.77, UNL.94
17 PLIP interactions:3 interactions with chain A, 11 interactions with chain C, 3 interactions with chain I- Hydrophobic interactions: A:F.197, A:F.197, A:L.297, C:L.386, C:L.386, I:F.28, I:F.28
- Hydrogen bonds: C:S.388, C:N.400, C:N.400, C:V.402, C:V.402, I:Y.32
- Water bridges: C:E.65, C:Q.66, C:G.67, C:G.67
DGD.68: 29 residues within 4Å:- Chain A: Q.199, L.200, A.203, W.278, F.300, N.301, F.302, S.305
- Chain C: L.386, 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.6, CLA.54, DGD.67, LHG.80, LMG.93
14 PLIP interactions:6 interactions with chain A, 4 interactions with chain C, 1 interactions with chain P, 3 interactions with chain I- Hydrophobic interactions: A:Q.199, A:L.200, A:A.203, A:W.278, A:F.300
- Hydrogen bonds: A:S.305, C:N.387, C:N.397, C:S.398, P:Q.34, I:G.36, I:S.38
- Water bridges: C:N.400, I:G.36
DGD.90: 28 residues within 4Å:- Chain B: Y.192, F.249, G.253, Y.257, Y.272, Q.273, S.276, Y.278, T.451, F.462
- Chain D: G.76, H.77, F.110, I.113, I.149, L.152, G.153, S.155, A.280, L.281
- Chain G: L.45, Y.48, N.49, V.59, S.60, W.61
- Ligands: CLA.22, CLA.28
20 PLIP interactions:7 interactions with chain D, 7 interactions with chain G, 6 interactions with chain B- Hydrophobic interactions: D:F.110, D:I.113, D:I.149, D:A.280, D:L.281, G:Y.48, G:Y.48, G:Y.48, B:F.249, B:Y.257, B:T.451, 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:Y.192
- 3 x CA: CALCIUM ION(Non-covalent)
CA.73: 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.102: 5 residues within 4Å:- Chain M: T.136, S.137, T.138, 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
CA.104: 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.31
- 5 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
LHG.79: 23 residues within 4Å:- 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.29
- Chain N: F.17, A.20, I.21
- Ligands: CLA.4, CLA.5, SQD.13, PL9.78, LHG.98
16 PLIP interactions:8 interactions with chain D, 5 interactions with chain K, 3 interactions with chain N- Hydrophobic interactions: D:F.247, D:I.249, D:F.251, D:F.260, D:F.260, K:Y.18, K:L.29, N:F.17, N:F.17, N:I.21
- Hydrogen bonds: D:S.252, D:S.252, D:N.253, K:N.13, K:N.13, K:T.15
LHG.80: 21 residues within 4Å:- Chain A: R.140, W.142, V.145, F.273, W.284
- 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.54, CLA.58, CLA.60, DGD.68, UNL.96
15 PLIP interactions:5 interactions with chain C, 7 interactions with chain A, 3 interactions with chain D- Hydrophobic interactions: C:W.18, C:W.18, C:W.425, A:W.142, A:V.145, A:F.273, A:W.284
- Hydrogen bonds: C:R.429, C:R.429, D:N.210, D:A.219, D:T.221
- Water bridges: A:R.140, A:R.140
- Salt bridges: A:R.140
LHG.84: 22 residues within 4Å:- Chain A: S.232, 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, T.267, M.271
- Chain K: L.23, I.24
- Ligands: CLA.27, CLA.31, CLA.33, LHG.98
12 PLIP interactions:6 interactions with chain B, 2 interactions with chain A, 2 interactions with chain K, 2 interactions with chain D- Hydrophobic interactions: B:W.4, B:Y.5, B:L.460, K:L.23, K:I.24
- Water bridges: B:R.6, B:R.6
- Salt bridges: B:R.6
- Hydrogen bonds: A:S.232, A:N.234, D:R.129, D:Y.131
LHG.85: 18 residues within 4Å:- Chain A: L.258, I.259, F.260, Y.262, A.263
- Chain D: F.17, V.18
- Chain E: T.4, T.5, G.6, E.7, R.8, P.9, F.10, S.11
- Chain F: R.18
- Ligands: CLA.6, PL9.16
12 PLIP interactions:1 interactions with chain A, 10 interactions with chain E, 1 interactions with chain F- Hydrophobic interactions: A:A.263, E:F.10
- Hydrogen bonds: E:T.4, E:T.4, E:T.5, E:G.6, E:E.7, E:E.7, E:F.10, E:S.11, E:S.11, F:R.18
LHG.98: 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.23, V.26
- Chain L: P.18, F.21
- Ligands: CLA.5, CLA.31, CLA.34, BCR.37, LMG.41, PL9.78, LHG.79, LHG.84
15 PLIP interactions:4 interactions with chain K, 1 interactions with chain L, 4 interactions with chain B, 3 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: K:V.26, L:P.18, B:W.4, B:W.4, D:W.256, D:F.260, D:F.263
- 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.87: 20 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: I.14, R.18, W.19, V.22, H.23, A.26, V.27, I.30
- Chain T: A.18, I.22
21 PLIP interactions:11 interactions with chain F, 2 interactions with chain T, 8 interactions with chain E,- Hydrophobic interactions: F:I.14, F:W.19, F:V.22, F:A.26, F:V.27, F:I.30, T:A.18, T:I.22, E:I.13, E:T.26, E:I.27, E:I.27
- Salt bridges: F:R.18, E:R.8, 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.106: 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.59, P:L.72, P:Y.75, P:Y.75, P:I.88, P:P.93, P:I.115, P:I.119
- Hydrogen bonds: P:N.49, 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., 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 chlorophyll 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 X: Q
Photosystem II reaction center protein Ycf12: 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
XR
YS
ZT
R - Membrane
-
We predict this structure to be a membrane protein.
SMTL ID : 5ws6.1 (1 other biounit)
Native XFEL structure of Photosystem II (preflash two-flash dataset
Photosystem II D1 protein
Photosystem II CP47 reaction center protein
Photosystem II CP43 chlorophyll 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 X
Photosystem II reaction center protein Ycf12
Photosystem II reaction center protein Z
Photosystem II protein Y
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