- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 2 x HEA: HEME-A(Non-covalent)
- 1 x CU: COPPER (II) ION(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)
PGV.6: 13 residues within 4Å:- Chain A: N.406, T.408, W.409
- Chain D: T.77, A.81, F.84
- Chain K: F.4, H.5, V.12
- Chain M: P.12, Q.15, A.16, L.19
16 PLIP interactions:5 interactions with chain M, 3 interactions with chain A, 4 interactions with chain D, 4 interactions with chain K- Hydrophobic interactions: M:P.12, M:P.12, M:Q.15, M:A.16, M:L.19, A:T.408, A:W.409, A:W.409, D:T.77, D:A.81, D:F.84, D:F.84, K:F.4, K:F.4, K:V.12
- Salt bridges: K:H.5
PGV.7: 29 residues within 4Å:- Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, P.200
- Chain C: H.7, V.9, G.18, A.22, M.25, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, S.87, F.91
- Ligands: PEK.36
18 PLIP interactions:8 interactions with chain A, 10 interactions with chain C- Hydrophobic interactions: A:F.148, A:L.152, A:P.200, C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.91
- Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:W.55
- Water bridges: A:A.93, C:M.81
- Salt bridges: A:R.96
PGV.30: 5 residues within 4Å:- Chain C: V.89, T.93, W.97, L.104
- Ligands: CHD.35
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:V.89, C:T.93, C:W.97, C:W.97, C:W.97
PGV.32: 26 residues within 4Å:- Chain C: N.48, M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232
- Ligands: CDL.33, DMU.38
28 PLIP interactions:26 interactions with chain C, 2 interactions with chain F- Hydrophobic interactions: C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:I.60, C:F.84, C:F.84, C:I.208, C:I.208, C:T.211, C:F.212, C:F.212, C:F.212, C:F.212
- Hydrogen bonds: C:S.63, C:R.219, C:F.231, C:G.232
- Water bridges: C:S.63, C:R.219, C:H.229, C:H.229, F:Q.12, F:E.17
- Salt bridges: C:R.219, C:R.219, C:H.229
- 3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)
TGL.8: 24 residues within 4Å:- Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, P.106, F.109, L.110, L.113, F.393, F.400, S.401, I.472
- Chain L: N.9, I.10, P.11, F.12, R.19, M.23, F.27, F.28, S.30
25 PLIP interactions:17 interactions with chain A, 8 interactions with chain L- Hydrophobic interactions: A:L.18, A:L.20, A:L.21, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:W.25, A:F.109, A:L.110, A:L.110, A:L.113, A:F.393, A:F.400, A:I.472, L:I.10, L:F.12, L:F.12, L:F.12, L:F.27, L:F.27, L:F.28, L:F.28
TGL.22: 16 residues within 4Å:- Chain A: F.346, V.350, T.354, N.422, F.426, H.429, F.430, L.433
- Chain B: L.7, G.8, L.28, V.31, F.32, S.35, L.39
- Chain I: R.43
20 PLIP interactions:10 interactions with chain A, 2 interactions with chain I, 8 interactions with chain B- Hydrophobic interactions: A:F.346, A:F.346, A:V.350, A:T.354, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, A:L.433, B:L.7, B:V.31, B:F.32, B:F.32, B:F.32, B:L.39
- Water bridges: I:R.43, B:G.8, B:F.9
- Salt bridges: I:R.43
TGL.42: 21 residues within 4Å:- Chain A: W.334, L.342, G.343, F.414, A.415, V.419
- Chain B: L.39, I.42, S.43, T.47, K.49
- Chain D: R.70, T.72, E.74, W.75, V.78, M.83, I.86
- Chain E: P.73
- Ligands: EDO.21, DMU.61
13 PLIP interactions:1 interactions with chain E, 6 interactions with chain D, 2 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: E:P.73, D:W.75, D:V.78, D:V.78, D:I.86, B:L.39, B:I.42, A:W.334, A:W.334, A:L.342
- Hydrogen bonds: D:W.75
- Water bridges: D:T.72
- Salt bridges: A:K.411
- 33 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.9: 6 residues within 4Å:- Chain A: F.505, E.507, P.508
- Chain F: R.56, I.57, W.73
Ligand excluded by PLIPEDO.10: 9 residues within 4Å:- Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498
- Chain D: Y.8
- Ligands: EDO.44
Ligand excluded by PLIPEDO.11: 6 residues within 4Å:- Chain A: V.485, D.486, L.487, T.488, T.489
- Ligands: EDO.44
Ligand excluded by PLIPEDO.12: 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.49
Ligand excluded by PLIPEDO.13: 3 residues within 4Å:- Chain A: K.265, T.489
- Chain F: I.70
Ligand excluded by PLIPEDO.14: 6 residues within 4Å:- Chain A: E.266, P.267, G.269, Y.270
- Chain F: S.67
- Ligands: EDO.49
Ligand excluded by PLIPEDO.15: 6 residues within 4Å:- Chain A: G.269, Y.270, M.271, G.272
- Chain B: Q.59, E.62
Ligand excluded by PLIPEDO.16: 6 residues within 4Å:- Chain A: H.256, T.259, K.265, T.490, N.491
- Ligands: EDO.50
Ligand excluded by PLIPEDO.17: 7 residues within 4Å:- Chain A: T.10, N.11, D.91, Y.502, H.503
- Chain C: V.9
- Ligands: EDO.65
Ligand excluded by PLIPEDO.18: 2 residues within 4Å:- Chain A: P.131, D.221
Ligand excluded by PLIPEDO.19: 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.9
Ligand excluded by PLIPEDO.20: 6 residues within 4Å:- Chain A: Y.260, Y.261, V.394, H.395, W.494
- Chain M: I.1
Ligand excluded by PLIPEDO.21: 6 residues within 4Å:- Chain A: N.331, I.332, W.334
- Chain B: L.46, T.48
- Ligands: TGL.42
Ligand excluded by PLIPEDO.26: 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.27: 3 residues within 4Å:- Chain B: T.125, L.135, F.206
Ligand excluded by PLIPEDO.28: 2 residues within 4Å:- Chain B: E.157
- Ligands: EDO.41
Ligand excluded by PLIPEDO.39: 9 residues within 4Å:- Chain C: W.144, S.148, D.153, H.156
- Chain F: A.1, S.2
- Chain G: A.13, R.14, R.17
Ligand excluded by PLIPEDO.40: 2 residues within 4Å:- Chain C: Q.2, H.68
Ligand excluded by PLIPEDO.41: 5 residues within 4Å:- Chain A: P.222
- Chain B: G.177
- Chain C: E.109
- Chain H: W.62
- Ligands: EDO.28
Ligand excluded by PLIPEDO.43: 9 residues within 4Å:- Chain A: L.495
- Chain D: Y.8, A.9, L.10, P.11
- Chain F: F.72, W.73
- Ligands: EDO.44, EDO.48
Ligand excluded by PLIPEDO.44: 11 residues within 4Å:- Chain A: T.484, T.488, L.495
- Chain D: D.7, Y.8, L.10, P.11, S.12
- Ligands: EDO.10, EDO.11, EDO.43
Ligand excluded by PLIPEDO.45: 6 residues within 4Å:- Chain D: K.118, L.121, D.122, W.135, N.140
- Chain K: P.45
Ligand excluded by PLIPEDO.46: 6 residues within 4Å:- Chain D: Y.19, D.23
- Chain E: W.23, R.26, K.27, N.30
Ligand excluded by PLIPEDO.48: 4 residues within 4Å:- Chain F: F.72, Q.80, R.81
- Ligands: EDO.43
Ligand excluded by PLIPEDO.49: 6 residues within 4Å:- Chain A: E.266
- Chain F: N.66, S.67, T.68
- Ligands: EDO.12, EDO.14
Ligand excluded by PLIPEDO.50: 7 residues within 4Å:- Chain A: T.489, T.490
- Chain F: S.67, T.68, V.69, W.71
- Ligands: EDO.16
Ligand excluded by PLIPEDO.51: 6 residues within 4Å:- Chain A: Y.510
- Chain F: P.36, K.37, T.39, N.47, L.48
Ligand excluded by PLIPEDO.52: 7 residues within 4Å:- Chain A: E.507
- Chain C: T.3
- Chain F: P.30, N.32, P.50, R.56, L.96
Ligand excluded by PLIPEDO.54: 5 residues within 4Å:- Chain G: P.49, Y.50, L.53, R.54, P.79
Ligand excluded by PLIPEDO.55: 5 residues within 4Å:- Chain C: F.33
- Chain G: K.58, P.59, F.60, S.61
Ligand excluded by PLIPEDO.58: 6 residues within 4Å:- Chain C: N.10, P.11
- Chain J: G.17, L.18, P.19
- Ligands: EDO.65
Ligand excluded by PLIPEDO.59: 7 residues within 4Å:- Chain A: V.118, E.119
- Chain J: A.53, S.54, F.55, P.56
- Chain L: K.45
Ligand excluded by PLIPEDO.65: 6 residues within 4Å:- Chain A: Y.502
- Chain C: P.11
- Chain L: H.1, Y.2
- Ligands: EDO.17, EDO.58
Ligand excluded by PLIP- 1 x CUA: DINUCLEAR COPPER ION(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)
- 10 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)
DMU.25: 7 residues within 4Å:- Chain B: H.26, M.29, I.30, L.33, I.34, L.37, I.72
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:I.30, B:I.34, B:L.37
DMU.31: 14 residues within 4Å:- Chain A: L.110, A.114
- Chain C: L.23, S.27, M.31, F.35
- Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52, A.53, K.58
12 PLIP interactions:4 interactions with chain C, 3 interactions with chain A, 5 interactions with chain J- Hydrophobic interactions: C:L.23, C:M.31, C:F.35, C:F.35, A:L.110, A:L.110, A:A.114, J:L.50, J:A.53
- Hydrogen bonds: J:Y.45, J:Y.45, J:K.58
DMU.38: 6 residues within 4Å:- Chain C: W.32, M.38, L.45
- Chain G: F.69
- Ligands: PGV.32, PEK.36
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:W.32, C:L.45
DMU.57: 5 residues within 4Å:- Chain C: T.39, I.43
- Chain J: G.41, G.42, Y.45
2 PLIP interactions:1 interactions with chain J, 1 interactions with chain C- Hydrophobic interactions: J:Y.45, C:T.39
DMU.60: 7 residues within 4Å:- Chain D: L.91, W.95, H.98, Y.99
- Chain K: Q.30, I.31, G.32
7 PLIP interactions:5 interactions with chain D, 2 interactions with chain K- Hydrophobic interactions: D:L.91, D:W.95
- Water bridges: D:K.97, D:H.98, K:G.32
- Salt bridges: D:H.98
- Hydrogen bonds: K:Q.30
DMU.61: 5 residues within 4Å:- Chain A: M.423
- Chain D: I.86
- Chain K: V.21, W.24
- Ligands: TGL.42
4 PLIP interactions:3 interactions with chain K, 1 interactions with chain D- Hydrophobic interactions: K:V.21, K:W.24, K:W.24, D:I.86
DMU.62: 4 residues within 4Å:- Chain K: A.28, T.29, W.35
- Ligands: DMU.63
1 PLIP interactions:1 interactions with chain K- Hydrophobic interactions: K:W.35
DMU.63: 3 residues within 4Å:- Chain K: W.24, A.28
- Ligands: DMU.62
2 PLIP interactions:2 interactions with chain K- Hydrophobic interactions: K:W.24, K:A.28
DMU.64: 2 residues within 4Å:- Chain K: F.19, A.22
2 PLIP interactions:2 interactions with chain K- Hydrophobic interactions: K:F.19, K:A.22
DMU.66: 13 residues within 4Å:- Chain A: L.35, F.459, L.462
- Chain D: L.92, W.95, Y.99
- Chain L: F.36
- Chain M: L.27, L.28, G.31, W.32, Y.35, H.36
12 PLIP interactions:4 interactions with chain M, 3 interactions with chain D, 1 interactions with chain L, 4 interactions with chain A- Hydrophobic interactions: M:L.27, D:L.92, D:W.95, D:W.95, L:F.36, A:L.35, A:F.459, A:F.459, A:L.462
- Water bridges: M:W.32, M:H.36, M:H.36
- 3 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)
PEK.29: 8 residues within 4Å:- Chain C: I.82, V.89, T.93, F.96, W.238, F.242, V.245, F.249
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:I.82, C:V.89, C:F.96, C:F.96, C:W.238, C:W.238, C:F.242, C:V.245
PEK.36: 25 residues within 4Å:- Chain A: H.151, V.155, T.207, L.210, L.215
- Chain C: W.32, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201, L.204
- Chain G: W.62, T.68, F.69, F.70, H.71, N.76
- Ligands: PGV.7, DMU.38
19 PLIP interactions:3 interactions with chain A, 9 interactions with chain C, 7 interactions with chain G- Hydrophobic interactions: A:V.155, A:L.210, A:L.215, C:W.32, C:W.32, C:Y.179, C:I.186, C:F.201, C:F.201, C:L.204, C:L.204, G:F.69
- Hydrogen bonds: C:I.186, G:T.68, G:F.70, G:N.76, G:N.76
- Water bridges: G:F.69, G:F.69
PEK.37: 9 residues within 4Å:- Chain C: Q.159, I.163, T.166, L.167, Y.170
- Chain G: F.21, G.22, P.26
- Ligands: CDL.53
9 PLIP interactions:4 interactions with chain G, 5 interactions with chain C- Hydrophobic interactions: G:F.21, G:F.21, G:F.21, G:P.26, C:I.163, C:T.166, C:L.167, C:Y.170, C:Y.170
- 2 x CDL: CARDIOLIPIN(Non-covalent)
CDL.33: 14 residues within 4Å:- Chain C: M.49, L.50, Y.53, W.56, R.57, I.60, V.169, T.172, L.173, T.211, I.214, V.215, F.218
- Ligands: PGV.32
18 PLIP interactions:18 interactions with chain C- Hydrophobic interactions: C:M.49, C:L.50, C:Y.53, C:Y.53, C:Y.53, C:Y.53, C:W.56, C:W.56, C:R.57, C:I.60, C:V.169, C:T.172, C:L.173, C:T.211, C:I.214, C:I.214, C:F.218
- Hydrogen bonds: C:Y.53
CDL.53: 17 residues within 4Å:- Chain C: L.125, L.129, T.132, S.133, V.140, L.248, Y.251, V.252, W.256
- Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38
- Ligands: PEK.37
12 PLIP interactions:7 interactions with chain C, 5 interactions with chain G- Hydrophobic interactions: C:L.129, C:L.129, C:T.132, C:L.248, C:Y.251, C:V.252, C:W.256, G:L.23, G:L.30, G:L.30, G:N.34, G:L.37
- 2 x CHD: CHOLIC ACID(Non-covalent)
CHD.34: 6 residues within 4Å:- Chain C: R.154, Q.159, F.162, F.217, L.221
- Chain J: F.1
9 PLIP interactions:3 interactions with chain J, 6 interactions with chain C- Hydrophobic interactions: J:F.1, C:F.162, C:F.162, C:F.162, C:F.217, C:L.221
- Hydrogen bonds: J:F.1, J:F.1
- Salt bridges: C:R.154
CHD.35: 8 residues within 4Å:- Chain A: H.233, W.288, D.300, T.301, Y.304
- Chain C: W.97, H.101
- Ligands: PGV.30
8 PLIP interactions:3 interactions with chain C, 5 interactions with chain A- Hydrophobic interactions: C:W.97, A:W.288, A:Y.304
- Hydrogen bonds: C:W.97, A:T.301
- Salt bridges: C:H.101, A:H.233
- Water bridges: A:T.301
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yano, N. et al., The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J.Biol.Chem. (2016)
- Release Date
- 2016-09-14
- Peptides
- Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 5B, mitochondrial: F
Cytochrome c oxidase subunit 6A2, mitochondrial: G
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A1, mitochondrial: J
Cytochrome c oxidase subunit 7B, mitochondrial: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8B, mitochondrial: M - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
NB
OC
PD
QE
RF
SG
TH
UI
VJ
WK
XL
YM
Z - Membrane
-
We predict this structure to be a membrane protein.
SMTL ID : 5b1b.2 (1 other biounit)
Bovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution
Cytochrome c oxidase subunit 1
Cytochrome c oxidase subunit 2
Cytochrome c oxidase subunit 3
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Cytochrome c oxidase subunit 5A, mitochondrial
Cytochrome c oxidase subunit 5B, mitochondrial
Cytochrome c oxidase subunit 6A2, mitochondrial
Cytochrome c oxidase subunit 6B1
Cytochrome c oxidase subunit 6C
Cytochrome c oxidase subunit 7A1, mitochondrial
Cytochrome c oxidase subunit 7B, mitochondrial
Cytochrome c oxidase subunit 7C, mitochondrial
Cytochrome c oxidase subunit 8B, mitochondrial
Related Entries With Identical Sequence
1occ.1 | 1oco.1 | 1ocr.1 | 1ocz.1 | 1v54.1 | 1v55.1 | 2dyr.1 | 2dys.1 | 2eij.1 | 2eik.1 | 2eil.1 | 2eim.1 | 2ein.1 | 2occ.1 | 2occ.2 | 2occ.3 | 2y69.1 | 2y69.2 | 2ybb.1 | 2zxw.1 | 2zxw.2 | 3abk.1 | 3abk.2 | 3abl.1 | 3abl.2 | 3abm.1 | 3abm.2 | 3ag1.1 | 3ag1.2 | 3ag2.1 more...less...3ag2.2 | 3ag3.1 | 3ag3.2 | 3ag4.1 | 3ag4.2 | 3asn.1 | 3asn.2 | 3aso.1 | 3aso.2 | 3wg7.1 | 3wg7.2 | 3x2q.1 | 3x2q.2 | 5b1a.1 | 5b1a.2 | 5b1b.1 | 5b3s.1 | 5b3s.2 | 5gpn.51 | 5gpn.52 | 5gpn.54 | 5gpn.59 | 5gpn.60 | 5gup.1 | 5gup.72 | 5gup.73 | 5gup.77 | 5gup.78 | 5iy5.1 | 5iy5.2 | 5luf.1 | 5w97.1 | 5wau.1 | 5x19.1 | 5x19.2 | 5x1b.1 | 5x1b.2 | 5x1f.1 | 5x1f.2 | 5xdq.1 | 5xdq.2 | 5xdx.1 | 5xdx.2 | 5xth.46 | 5xth.47 | 5xth.49 | 5xth.51 | 5xth.52 | 5xth.54 | 5xth.56 | 5xth.58 | 5xti.46 | 5xti.47 | 5xti.49 | 5xti.51 | 5xti.52 | 5xti.54 | 5xti.56 | 5xti.58 | 5xti.126 | 5xti.127 | 5xti.129 | 5xti.131 | 5xti.132 | 5xti.134 | 5xti.136 | 5xti.138 | 5z84.1 | 5z84.2 | 5z85.1 | 5z85.2 | 5z86.1 | 5z86.2 | 5zco.1 | 5zco.2 | 5zcp.1 | 5zcp.2 | 5zcq.1 | 5zcq.2 | 6j8m.1 | 6j8m.2 | 6juw.1 | 6jy3.1 | 6jy4.1 | 6nkn.1 | 6nmf.1 | 6nmp.1 | 7coh.1 | 7coh.2 | 7cp5.1 | 7d5w.1 | 7d5x.1 | 7dgr.67 | 7dgr.68 | 7dgs.67 | 7dgs.68 | 7dkf.68 | 7dkf.69 | 7ev7.1 | 7ev7.2 | 7thu.1 | 7tie.1 | 7tih.1 | 7tii.1 | 7vuw.1 | 7vuw.2 | 7vvr.1 | 7vvr.2 | 7w3e.1 | 7w3e.2 | 7xma.1 | 7xma.2 | 7xmb.1 | 7xmb.2 | 7y44.1 | 7y44.2 | 7ypy.1 | 7ypy.2 | 8d4t.1 | 8gbt.1 | 8gcq.1 | 8gvm.1 | 8gvm.2 | 8h8r.1 | 8h8s.1 | 8ijn.1 | 8ijn.2