- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)
- 2 x HEA: HEME-A(Non-covalent)
HEA.2: 36 residues within 4Å:- Chain A: A.24, G.27, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468
- Ligands: TGL.95
37 PLIP interactions:37 interactions with chain A,- Hydrophobic interactions: A:A.24, A:T.31, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:I.389, A:F.393, A:F.393, A:T.424, A:F.425, A:F.425, A:V.465
- Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440
- Water bridges: A:R.438, A:R.438, A:S.461
- Salt bridges: A:R.438, A:R.439
- pi-Stacking: A:F.377, A:F.425
- Metal complexes: A:H.61, A:H.378
HEA.3: 34 residues within 4Å:- Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438
- Chain B: I.34, P.69, I.72, L.73
- Ligands: CMO.7
36 PLIP interactions:5 interactions with chain B, 31 interactions with chain A,- Hydrophobic interactions: B:I.34, B:I.34, B:P.69, B:I.72, B:L.73, A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:T.316, A:V.320, A:F.348, A:I.356, A:I.356, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381
- Hydrogen bonds: A:W.126, A:Y.244
- Water bridges: A:H.291, A:T.316, A:D.369, A:D.369, A:R.439
- Salt bridges: A:H.368, A:R.438, A:R.439
- pi-Cation interactions: A:H.240
- Metal complexes: A:H.376
- 1 x CU: COPPER (II) ION(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 1 x CMO: CARBON MONOXIDE(Non-functional Binders)
- 71 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.9: 8 residues within 4Å:- Chain A: Y.19, N.80, M.92, N.98, S.101, G.160, N.163, F.164
Ligand excluded by PLIPEDO.10: 6 residues within 4Å:- Chain A: H.256, T.259, K.265, T.490, N.491
- Ligands: EDO.72
Ligand excluded by PLIPEDO.11: 7 residues within 4Å:- Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494
- Chain M: I.1
Ligand excluded by PLIPEDO.12: 5 residues within 4Å:- Chain A: L.136, A.137
- Chain B: Q.103, W.104
- Ligands: EDO.21
Ligand excluded by PLIPEDO.13: 5 residues within 4Å:- Chain A: K.265, T.489
- Chain F: I.70, P.83, S.84
Ligand excluded by PLIPEDO.14: 4 residues within 4Å:- Chain A: K.333, T.484
- Chain M: I.1, T.2
Ligand excluded by PLIPEDO.15: 5 residues within 4Å:- Chain A: V.485, D.486, L.487, T.488, T.489
Ligand excluded by PLIPEDO.16: 2 residues within 4Å:- Chain A: P.131, D.221
Ligand excluded by PLIPEDO.17: 8 residues within 4Å:- Chain A: K.265, E.266
- Chain B: T.55
- Chain F: N.66, T.68, I.70, S.84
- Ligands: EDO.73
Ligand excluded by PLIPEDO.18: 8 residues within 4Å:- Chain A: G.269, Y.270, M.271, G.272
- Chain B: A.58, E.62
- Ligands: CHD.30, EDO.38
Ligand excluded by PLIPEDO.19: 7 residues within 4Å:- Chain A: E.266, P.267, G.269, Y.270
- Chain F: S.67
- Ligands: EDO.38, EDO.73
Ligand excluded by PLIPEDO.20: 9 residues within 4Å:- Chain A: R.5, N.11, K.13, D.14, W.81, P.499, P.500, Y.502
- Chain L: N.10
Ligand excluded by PLIPEDO.21: 6 residues within 4Å:- Chain A: Q.52, A.120, A.137, H.138, A.139
- Ligands: EDO.12
Ligand excluded by PLIPEDO.22: 3 residues within 4Å:- Chain A: E.119, A.139, G.140
Ligand excluded by PLIPEDO.23: 7 residues within 4Å:- Chain A: Q.43, P.44, G.45, T.46, L.47
- Chain D: Y.104, P.106
Ligand excluded by PLIPEDO.24: 1 residues within 4Å:- Ligands: TGL.95
Ligand excluded by PLIPEDO.25: 2 residues within 4Å:- Chain A: Y.304
- Ligands: PGV.48
Ligand excluded by PLIPEDO.26: 7 residues within 4Å:- Chain A: V.482, L.483, G.497, C.498
- Chain D: S.8, Y.11
- Ligands: EDO.62
Ligand excluded by PLIPEDO.27: 7 residues within 4Å:- Chain A: Y.19, M.71, P.72, S.101, L.105, S.156, S.157
Ligand excluded by PLIPEDO.32: 2 residues within 4Å:- Chain B: T.125, F.206
Ligand excluded by PLIPEDO.33: 7 residues within 4Å:- Chain A: Y.447
- Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193
Ligand excluded by PLIPEDO.34: 6 residues within 4Å:- Chain B: E.132, R.141
- Chain I: I.68, F.69, Q.70, K.73
Ligand excluded by PLIPEDO.35: 5 residues within 4Å:- Chain B: W.104, Y.121, M.122, N.203, F.206
Ligand excluded by PLIPEDO.36: 4 residues within 4Å:- Chain B: I.123, E.127, K.129, E.132
Ligand excluded by PLIPEDO.37: 6 residues within 4Å:- Chain B: Y.3, Q.6, L.7, G.8, F.9
- Ligands: TGL.28
Ligand excluded by PLIPEDO.38: 5 residues within 4Å:- Chain B: T.55, M.56, A.58
- Ligands: EDO.18, EDO.19
Ligand excluded by PLIPEDO.39: 6 residues within 4Å:- Chain B: F.118, N.140, R.141, W.222, M.226
- Chain I: Q.70
Ligand excluded by PLIPEDO.40: 4 residues within 4Å:- Chain B: E.157, P.176
- Ligands: EDO.53, EDO.87
Ligand excluded by PLIPEDO.41: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPEDO.53: 7 residues within 4Å:- Chain A: P.222
- Chain B: G.177
- Chain C: E.111
- Chain H: W.68
- Ligands: EDO.40, EDO.57, EDO.87
Ligand excluded by PLIPEDO.54: 5 residues within 4Å:- Chain C: N.12, Q.68
- Chain J: L.18, V.20, K.23
Ligand excluded by PLIPEDO.55: 3 residues within 4Å:- Chain C: H.3, Q.4, H.70
Ligand excluded by PLIPEDO.56: 9 residues within 4Å:- Chain C: W.146, S.150, D.155, H.158
- Chain F: A.1, S.2
- Chain G: A.13, R.14, R.17
Ligand excluded by PLIPEDO.57: 6 residues within 4Å:- Chain B: G.177
- Chain C: E.111
- Chain H: W.68, W.72
- Ligands: EDO.53, EDO.87
Ligand excluded by PLIPEDO.58: 4 residues within 4Å:- Chain C: P.73, Q.76, K.77, R.80
Ligand excluded by PLIPEDO.59: 5 residues within 4Å:- Chain C: T.145, H.148, A.239, W.240, H.243
Ligand excluded by PLIPEDO.62: 8 residues within 4Å:- Chain A: L.483, T.484
- Chain D: V.6, K.7, D.10, Y.11, S.15
- Ligands: EDO.26
Ligand excluded by PLIPEDO.63: 3 residues within 4Å:- Chain D: K.137
- Chain K: S.43, V.45
Ligand excluded by PLIPEDO.64: 4 residues within 4Å:- Chain D: V.30, E.58, R.61, L.62
Ligand excluded by PLIPEDO.65: 5 residues within 4Å:- Chain D: S.36, A.39, L.40, E.55, E.58
Ligand excluded by PLIPEDO.66: 4 residues within 4Å:- Chain D: K.31, N.32, L.33, K.38
Ligand excluded by PLIPEDO.67: 6 residues within 4Å:- Chain D: K.121, L.124, D.125, W.138, N.143
- Chain K: P.50
Ligand excluded by PLIPEDO.68: 3 residues within 4Å:- Chain E: Y.82, P.83, E.102
Ligand excluded by PLIPEDO.69: 7 residues within 4Å:- Chain D: Y.22, D.26
- Chain E: W.27, R.30, K.31, N.34
- Chain F: P.83
Ligand excluded by PLIPEDO.70: 4 residues within 4Å:- Chain E: Y.18, K.21, I.24, E.28
Ligand excluded by PLIPEDO.72: 7 residues within 4Å:- Chain A: T.489, T.490
- Chain F: S.67, T.68, V.69, W.71
- Ligands: EDO.10
Ligand excluded by PLIPEDO.73: 7 residues within 4Å:- Chain A: E.266
- Chain F: D.65, N.66, S.67, T.68
- Ligands: EDO.17, EDO.19
Ligand excluded by PLIPEDO.74: 6 residues within 4Å:- Chain A: Y.510
- Chain F: P.36, K.37, T.39, N.47, L.48
Ligand excluded by PLIPEDO.75: 5 residues within 4Å:- Chain F: A.1
- Chain G: R.14, R.17
- Ligands: PEK.46, CHD.79
Ligand excluded by PLIPEDO.76: 3 residues within 4Å:- Chain C: H.231
- Chain F: D.9, E.17
Ligand excluded by PLIPEDO.77: 4 residues within 4Å:- Chain C: F.225
- Chain F: G.5, P.7
- Chain J: N.3
Ligand excluded by PLIPEDO.80: 4 residues within 4Å:- Chain G: K.5, F.18, G.22, L.23
Ligand excluded by PLIPEDO.81: 4 residues within 4Å:- Chain G: L.30, L.33, N.34
- Ligands: CDL.78
Ligand excluded by PLIPEDO.82: 4 residues within 4Å:- Chain C: F.35
- Chain G: K.58, P.59, S.61
Ligand excluded by PLIPEDO.83: 6 residues within 4Å:- Chain C: G.120
- Chain G: A.46, F.47, I.48, L.53, R.54
Ligand excluded by PLIPEDO.84: 6 residues within 4Å:- Chain G: G.10, T.11, G.12, A.13, R.14, T.15
Ligand excluded by PLIPEDO.86: 7 residues within 4Å:- Chain B: S.94, L.95, Y.113, M.148, L.216, F.219
- Chain H: Q.12
Ligand excluded by PLIPEDO.87: 5 residues within 4Å:- Chain H: S.67, T.71
- Ligands: EDO.40, EDO.53, EDO.57
Ligand excluded by PLIPEDO.88: 6 residues within 4Å:- Chain A: D.227
- Chain B: G.177, R.178
- Chain C: T.109
- Chain H: N.24, T.26
Ligand excluded by PLIPEDO.91: 2 residues within 4Å:- Chain J: Y.32
- Ligands: CHD.90
Ligand excluded by PLIPEDO.92: 3 residues within 4Å:- Chain J: Q.9, K.10, Q.13
Ligand excluded by PLIPEDO.93: 3 residues within 4Å:- Chain A: M.423
- Chain D: I.89
- Chain K: W.29
Ligand excluded by PLIPEDO.94: 7 residues within 4Å:- Chain D: N.76, K.79
- Chain K: H.10, D.11, K.12, G.14, N.15
Ligand excluded by PLIPEDO.96: 4 residues within 4Å:- Chain L: T.26, G.30
- Chain M: S.25
- Ligands: DMU.105
Ligand excluded by PLIPEDO.97: 3 residues within 4Å:- Chain A: M.117
- Chain L: F.38
- Ligands: EDO.98
Ligand excluded by PLIPEDO.98: 3 residues within 4Å:- Chain L: R.41, H.42
- Ligands: EDO.97
Ligand excluded by PLIPEDO.99: 3 residues within 4Å:- Chain L: S.31, F.38
- Ligands: TGL.95
Ligand excluded by PLIPEDO.101: 5 residues within 4Å:- Chain A: T.46, L.47
- Chain D: V.103
- Chain M: D.38, K.41
Ligand excluded by PLIPEDO.102: 3 residues within 4Å:- Chain A: D.407
- Chain M: I.1
- Ligands: PGV.1
Ligand excluded by PLIPEDO.103: 5 residues within 4Å:- Chain A: E.481
- Chain D: S.8
- Chain M: K.4, K.7
- Ligands: EDO.104
Ligand excluded by PLIPEDO.104: 4 residues within 4Å:- Chain D: V.6
- Chain M: K.4, K.7
- Ligands: EDO.103
Ligand excluded by PLIP- 3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)
TGL.28: 15 residues within 4Å:- Chain A: F.346, V.350, Y.379, N.422, F.426, F.430, L.433
- Chain B: L.7, G.8, L.28, F.32, S.35, L.39
- Chain I: R.43
- Ligands: EDO.37
13 PLIP interactions:6 interactions with chain A, 6 interactions with chain B, 1 interactions with chain I- Hydrophobic interactions: A:F.346, A:F.426, A:F.426, A:F.426, A:F.426, A:F.430, B:L.7, B:F.32, B:F.32, B:L.39
- Water bridges: B:F.9
- Salt bridges: B:H.24, I:R.43
TGL.61: 23 residues within 4Å:- Chain A: W.334, M.339, L.342, G.343, F.346, F.414, A.415, V.419
- Chain B: L.39, I.42, L.46, T.47, K.49
- Chain D: R.73, S.74, T.75, E.77, W.78, V.81, M.86, I.89
- Chain I: R.16, H.20
19 PLIP interactions:9 interactions with chain A, 4 interactions with chain B, 6 interactions with chain D- Hydrophobic interactions: A:W.334, A:W.334, A:W.334, A:L.342, A:F.346, A:F.414, A:A.415, A:V.419, B:L.39, B:I.42, B:L.46, B:K.49, D:E.77, D:V.81, D:I.89
- Salt bridges: A:K.411
- Hydrogen bonds: D:E.77, D:W.78
- Water bridges: D:T.75
TGL.95: 26 residues within 4Å:- Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, F.109, L.113, F.393, F.400, S.401, I.472
- Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, F.28, F.29, S.31
- Ligands: HEA.2, EDO.24, EDO.99
21 PLIP interactions:12 interactions with chain A, 9 interactions with chain L- Hydrophobic interactions: A:T.17, A:L.18, A:L.20, A:L.21, A:F.22, A:F.22, A:W.25, A:F.109, A:L.113, A:F.393, A:I.472, A:I.472, L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.28, L:F.29, L:F.29
- 1 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)
PSC.29: 22 residues within 4Å:- Chain A: F.268, F.321, L.324, A.325, H.328
- Chain B: L.37, I.41, H.52, M.56, D.57, E.60, V.61, I.64
- Chain E: E.6, T.7, D.8, F.11, D.40, L.41
- Chain I: R.10, A.14, L.17
20 PLIP interactions:3 interactions with chain I, 5 interactions with chain A, 9 interactions with chain B, 3 interactions with chain E- Hydrophobic interactions: I:L.17, A:F.268, A:F.321, A:F.321, A:L.324, A:A.325, B:L.37, B:I.41, B:I.41, B:M.56, B:D.57, B:V.61, B:I.64
- Hydrogen bonds: I:G.11
- Water bridges: I:A.14, E:D.40
- Salt bridges: B:H.52, B:H.52, E:D.8
- pi-Cation interactions: E:F.11
- 6 x CHD: CHOLIC ACID(Non-covalent)
CHD.30: 7 residues within 4Å:- Chain A: M.271, G.272, W.275
- Chain B: E.62, T.63, T.66
- Ligands: EDO.18
8 PLIP interactions:4 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:T.66, A:M.271, A:W.275, A:W.275, A:W.275
- Hydrogen bonds: B:E.62, B:T.63
- Water bridges: B:T.63
CHD.42: 9 residues within 4Å:- Chain A: H.233, W.288, D.300, T.301, Y.304, F.305
- Chain C: W.99, H.103
- Ligands: PGV.48
9 PLIP interactions:3 interactions with chain C, 6 interactions with chain A- Hydrophobic interactions: C:W.99, A:W.288, A:Y.304, A:F.305
- Hydrogen bonds: C:W.99, A:T.301
- Salt bridges: C:H.103, A:H.233
- Water bridges: A:T.301
CHD.50: 6 residues within 4Å:- Chain C: R.156, L.160, F.164, F.219, L.223
- Chain J: F.1
8 PLIP interactions:1 interactions with chain J, 7 interactions with chain C- Hydrogen bonds: J:F.1
- Hydrophobic interactions: C:L.160, C:F.164, C:F.164, C:F.164, C:F.219, C:L.223
- Salt bridges: C:R.156
CHD.52: 6 residues within 4Å:- Chain C: W.116, P.117, V.254, W.258, W.259, S.261
2 PLIP interactions:2 interactions with chain C- Water bridges: C:W.259, C:S.261
CHD.79: 7 residues within 4Å:- Chain G: R.14, R.17, F.18, F.21, G.22
- Ligands: PEK.46, EDO.75
5 PLIP interactions:5 interactions with chain G- Hydrophobic interactions: G:F.21
- Water bridges: G:R.17, G:R.17
- Salt bridges: G:R.14, G:R.17
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)
- 2 x HEA: HEME-A(Non-covalent)
- 1 x CU: COPPER (II) ION(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 1 x CMO: CARBON MONOXIDE(Non-functional Binders)
- 71 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)
- 1 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)
- 6 x CHD: CHOLIC ACID(Non-covalent)