- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.45 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 4 x HEA: HEME-A(Non-covalent)
- 2 x CU: COPPER (II) ION(Non-covalent)
CU.3: 4 residues within 4Å:- Chain A: H.240, H.290, H.291
- Ligands: OH.10
5 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: A:H.240, A:H.290, A:H.291, H2O.1, OH.10
CU.35: 4 residues within 4Å:- Chain N: H.240, H.290, H.291
- Ligands: OH.40
5 PLIP interactions:3 interactions with chain N, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: N:H.240, N:H.290, N:H.291, H2O.21, OH.40
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.4: 4 residues within 4Å:- Chain A: H.368, D.369
- Chain B: S.197, E.198
5 PLIP interactions:1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: B:E.198, A:H.368, H2O.6, H2O.7, H2O.7
MG.36: 4 residues within 4Å:- Chain N: H.368, D.369
- Chain O: S.197, E.198
6 PLIP interactions:1 interactions with chain O, 2 interactions with chain N, 3 Ligand-Water interactions- Metal complexes: O:E.198, N:H.368, N:D.369, H2O.25, H2O.25, H2O.26
- 2 x NA: SODIUM ION(Non-functional Binders)
- 8 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)
PGV.6: 24 residues within 4Å:- Chain A: F.94, P.95, R.96, M.97, M.100, V.155
- Chain C: H.9, V.11, G.20, T.28, N.50, T.53, W.57, W.58, V.61, E.64, H.71, V.75, L.79, F.86, S.89, E.90
- Ligands: PEK.14, PGV.15
14 PLIP interactions:4 interactions with chain A, 10 interactions with chain C- Hydrophobic interactions: A:V.155, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86
- Hydrogen bonds: A:R.96, A:M.97, C:H.9, C:W.57
- Salt bridges: A:R.96
- Water bridges: C:M.83
PGV.7: 17 residues within 4Å:- Chain A: N.406, T.408, W.409, R.480
- Chain D: T.80, A.84, F.87, F.88
- Chain K: F.9, H.10
- Chain M: K.4, P.5, P.12, Q.15, A.16, L.19, S.20
15 PLIP interactions:5 interactions with chain D, 3 interactions with chain K, 5 interactions with chain A, 2 interactions with chain M- Hydrophobic interactions: D:T.80, D:A.84, D:F.87, D:F.87, D:F.88, K:F.9, K:F.9, A:T.408, A:W.409, A:W.409, A:W.409, M:P.12, M:L.19
- Salt bridges: K:H.10
- Hydrogen bonds: A:T.408
PGV.15: 23 residues within 4Å:- Chain C: M.51, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234
- Ligands: PGV.6, CDL.16
25 PLIP interactions:1 interactions with chain F, 24 interactions with chain C- Water bridges: F:E.17, C:R.221, C:H.231
- Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:F.86, C:I.210, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214
- Hydrogen bonds: C:S.65, C:H.71, C:R.221, C:F.233, C:G.234
- Salt bridges: C:R.221, C:R.221, C:H.231
PGV.20: 10 residues within 4Å:- Chain A: F.237, D.298
- Chain C: W.99, Y.102, H.103, L.106
- Chain H: N.22, N.24
- Ligands: CHD.18, CDL.57
5 PLIP interactions:1 interactions with chain A, 3 interactions with chain C, 1 interactions with chain H- Hydrophobic interactions: A:F.237, C:W.99, C:W.99
- Salt bridges: C:H.103
- Hydrogen bonds: H:N.22
PGV.43: 25 residues within 4Å:- Chain N: F.94, P.95, R.96, M.97, M.100
- Chain P: H.9, G.20, S.23, A.24, L.31, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, E.90, F.93
- Ligands: PGV.45, PEK.54
15 PLIP interactions:4 interactions with chain N, 11 interactions with chain P- Hydrogen bonds: N:R.96, N:M.97, P:H.9, P:W.57, P:E.64
- Water bridges: N:A.93
- Salt bridges: N:R.96
- Hydrophobic interactions: P:A.24, P:L.31, P:W.57, P:W.57, P:W.57, P:W.58, P:F.86, P:F.93
PGV.44: 12 residues within 4Å:- Chain C: W.258
- Chain G: A.1
- Chain N: F.237, D.298
- Chain P: V.91, W.99, H.103, A.107
- Chain U: N.22, N.24
- Ligands: CDL.26, CHD.48
10 PLIP interactions:4 interactions with chain U, 1 interactions with chain C, 4 interactions with chain P, 1 interactions with chain N- Hydrogen bonds: U:N.22, U:N.24
- Water bridges: U:N.22, U:N.24
- Hydrophobic interactions: C:W.258, P:V.91, P:W.99, P:W.99, N:F.237
- Salt bridges: P:H.103
PGV.45: 24 residues within 4Å:- Chain P: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234
- Ligands: PGV.43, CDL.46
26 PLIP interactions:25 interactions with chain P, 1 interactions with chain S- Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:W.58, P:W.58, P:I.62, P:F.86, P:I.210, P:I.210, P:I.210, P:T.213, P:F.214, P:F.214, P:F.214
- Hydrogen bonds: P:S.65, P:R.221, P:F.233, P:G.234
- Water bridges: P:R.221, P:H.231, P:H.231, S:E.17
- Salt bridges: P:R.221, P:R.221, P:H.231
PGV.63: 15 residues within 4Å:- Chain N: N.406, T.408, W.409, I.412, R.480
- Chain Q: A.84
- Chain X: F.9, H.10
- Chain Z: A.3, K.4, P.5, P.12, Q.15, A.16, S.20
12 PLIP interactions:5 interactions with chain N, 4 interactions with chain Z, 1 interactions with chain Q, 2 interactions with chain X- Hydrophobic interactions: N:W.409, N:W.409, N:I.412, Z:P.12, Z:P.12, Q:A.84, X:F.9
- Hydrogen bonds: N:T.408
- Water bridges: N:T.404, Z:A.3, Z:A.6
- Salt bridges: X:H.10
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 6 residues within 4Å:- Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.260, A:Y.261, A:H.395
EDO.9: 6 residues within 4Å:- Chain A: E.507
- Chain C: T.5
- Chain F: P.30, N.32, P.50, R.56
3 PLIP interactions:1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain F- Hydrogen bonds: C:T.5, A:E.507, F:N.32
EDO.21: 8 residues within 4Å:- Chain C: W.146, S.150, D.155, H.158
- Chain F: A.1
- Chain G: A.13, R.14, R.17
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain F- Hydrogen bonds: C:S.150, F:A.1
EDO.29: 5 residues within 4Å:- Chain C: G.120
- Chain G: A.46, F.47, I.48, R.54
5 PLIP interactions:4 interactions with chain G, 1 interactions with chain C- Hydrogen bonds: G:A.46, G:I.48, G:R.54, G:R.54, C:G.120
EDO.39: 7 residues within 4Å:- Chain N: Y.260, Y.261, V.394, H.395, P.398, W.494
- Chain Z: I.1
3 PLIP interactions:3 interactions with chain N- Hydrogen bonds: N:Y.260, N:V.394, N:H.395
EDO.51: 7 residues within 4Å:- Chain N: E.507
- Chain P: T.5
- Chain S: P.30, N.32, P.50, R.56, L.96
3 PLIP interactions:1 interactions with chain N, 2 interactions with chain S- Hydrogen bonds: N:E.507, S:P.30, S:N.32
EDO.52: 7 residues within 4Å:- Chain P: W.146, S.150, H.158
- Chain S: A.1
- Chain T: A.13, R.14, R.17
2 PLIP interactions:1 interactions with chain P, 1 interactions with chain S- Hydrogen bonds: P:W.146, S:A.1
EDO.58: 8 residues within 4Å:- Chain P: G.120
- Chain T: P.45, A.46, F.47, I.48, L.53, R.54, Y.82
4 PLIP interactions:3 interactions with chain T, 1 interactions with chain P- Hydrogen bonds: T:I.48, T:R.54, T:R.54, P:G.120
- 2 x OH: HYDROXIDE ION(Non-covalent)
- 6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)
TGL.11: 15 residues within 4Å:- Chain A: F.346, Y.379, N.422, F.426, F.430, L.433, W.450
- Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35
- Chain I: R.43
10 PLIP interactions:3 interactions with chain B, 6 interactions with chain A, 1 interactions with chain I- Hydrophobic interactions: B:V.31, A:F.346, A:F.426, A:F.426, A:F.430, A:L.433, A:W.450
- Hydrogen bonds: B:G.8
- Water bridges: B:F.9
- Salt bridges: I:R.43
TGL.22: 18 residues within 4Å:- Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415
- Chain B: I.42, S.43, T.47, K.49
- Chain D: R.73, T.75, E.77, W.78, V.81
- Chain I: R.16, H.20
10 PLIP interactions:6 interactions with chain A, 1 interactions with chain B, 3 interactions with chain D- Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:F.414, A:A.415, B:I.42, D:W.78, D:V.81
- Salt bridges: A:K.411
- Hydrogen bonds: D:W.78
TGL.32: 20 residues within 4Å:- Chain A: F.2, T.17, L.18, L.21, F.22, W.25, W.81, F.393, F.397, F.400, I.472
- Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29
17 PLIP interactions:8 interactions with chain A, 9 interactions with chain L- Hydrophobic interactions: A:F.2, A:L.18, A:F.22, A:W.25, A:W.81, A:F.393, A:F.397, A:F.400,
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.45 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 4 x HEA: HEME-A(Non-covalent)
- 2 x CU: COPPER (II) ION(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 8 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x OH: HYDROXIDE ION(Non-covalent)
- 6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)