- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 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)
- 2 x AZI: AZIDE ION(Non-covalent)
AZI.6: 7 residues within 4Å:- Chain A: H.240, Y.244, H.290, T.309
- Ligands: HEA.2, CU.3, AZI.7
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.244
- Water bridges: A:Y.244
AZI.7: 8 residues within 4Å:- Chain A: G.239, H.240, V.243, H.290, H.291
- Ligands: HEA.2, CU.3, AZI.6
No protein-ligand interaction detected (PLIP)- 3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)
TGL.8: 15 residues within 4Å:- Chain A: T.354, N.422, F.426, H.429, F.430, L.433
- Chain B: L.7, G.8, H.24, L.28, F.32, S.35, S.36, L.39
- Chain I: R.43
14 PLIP interactions:8 interactions with chain A, 4 interactions with chain B, 2 interactions with chain I- Hydrophobic interactions: A:T.354, A:N.422, A:F.426, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, B:L.7, B:F.32, B:L.39
- Salt bridges: B:H.24, I:R.43
- Water bridges: I:R.43
TGL.11: 24 residues within 4Å:- Chain A: F.2, T.17, L.20, L.21, F.22, W.25, F.102, P.106, L.113, F.393, F.400, S.401, I.472, F.476
- Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29
22 PLIP interactions:16 interactions with chain A, 6 interactions with chain L- Hydrophobic interactions: A:F.2, A:F.2, A:F.2, A:T.17, A:L.20, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:F.102, A:L.113, A:F.393, A:F.400, A:I.472, A:F.476, L:I.11, L:F.13, L:F.13, L:F.28, L:F.29, L:F.29
TGL.40: 21 residues within 4Å:- Chain A: W.334, M.339, L.342, G.343, F.346, F.414, A.415, V.419
- Chain B: I.42, 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
15 PLIP interactions:6 interactions with chain D, 9 interactions with chain A- Hydrophobic interactions: D:V.81, D:I.89, A:W.334, A:W.334, A:W.334, A:L.342, A:F.346, A:F.414, A:A.415, A:V.419
- Hydrogen bonds: D:T.75, D:W.78
- Water bridges: D:T.75, D:T.75
- Salt bridges: A:K.411
- 4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)
PGV.9: 31 residues within 4Å:- Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, I.158, L.159, P.200
- Chain C: H.9, V.11, G.20, A.24, M.27, T.28, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, E.90
- Ligands: PGV.31, PEK.50
16 PLIP interactions:8 interactions with chain A, 8 interactions with chain C- Hydrophobic interactions: A:F.148, A:L.152, A:I.158, A:L.159, A:P.200, C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58
- Hydrogen bonds: A:R.96, A:M.97
- Salt bridges: A:R.96
- Water bridges: C:M.83
PGV.10: 12 residues within 4Å:- Chain A: N.406, T.408, W.409
- Chain D: A.84, F.87
- Chain K: F.9, H.10
- Chain M: P.12, Q.15, A.16, L.19, S.20
18 PLIP interactions:4 interactions with chain D, 6 interactions with chain A, 4 interactions with chain M, 4 interactions with chain K- Hydrophobic interactions: D:A.84, D:F.87, D:F.87, D:F.87, A:T.408, A:W.409, A:W.409, A:W.409, M:P.12, M:Q.15, M:A.16, M:L.19, K:F.9, K:F.9, K:F.9
- Hydrogen bonds: A:T.408
- Water bridges: A:R.480
- Salt bridges: K:H.10
PGV.31: 27 residues within 4Å:- Chain C: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, M.83, F.86, E.90, L.206, 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.9, CDL.32
30 PLIP interactions:28 interactions with chain C, 2 interactions with chain F- Hydrophobic interactions: C:W.58, 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:L.206, C:I.210, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214
- Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234
- Water bridges: C:S.65, C:R.221, C:H.231, C:H.231, F:Q.12, F:E.17
- Salt bridges: C:R.221, C:R.221, C:H.231
PGV.35: 9 residues within 4Å:- Chain C: T.95, W.99, H.103, A.107
- Chain H: F.20, N.24, R.27
- Ligands: EDO.15, CHD.28
5 PLIP interactions:2 interactions with chain H, 3 interactions with chain C- Water bridges: H:N.22, H:N.24
- Hydrophobic interactions: C:W.99, C:W.99
- Hydrogen bonds: C:H.103
- 26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.12: 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.13: 5 residues within 4Å:- Chain A: Q.52, A.120, A.137, H.138, A.139
Ligand excluded by PLIPEDO.14: 6 residues within 4Å:- Chain A: H.256, T.259, K.265, T.490, N.491
- Ligands: EDO.47
Ligand excluded by PLIPEDO.15: 4 residues within 4Å:- Chain A: W.288, Y.304
- Ligands: CHD.28, PGV.35
Ligand excluded by PLIPEDO.16: 8 residues within 4Å:- Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494
- Chain M: I.1
- Ligands: EDO.19
Ligand excluded by PLIPEDO.17: 5 residues within 4Å:- Chain A: K.265, T.489
- Chain F: I.70, P.83, S.84
Ligand excluded by PLIPEDO.18: 7 residues within 4Å:- Chain A: K.265, E.266
- Chain B: T.55
- Chain F: N.66, T.68, I.70, S.84
Ligand excluded by PLIPEDO.19: 5 residues within 4Å:- Chain A: Y.261, S.335, D.407
- Chain M: I.1
- Ligands: EDO.16
Ligand excluded by PLIPEDO.20: 6 residues within 4Å:- Chain A: E.507
- Chain C: T.5
- Chain F: P.30, N.32, P.50, R.56
Ligand excluded by PLIPEDO.24: 2 residues within 4Å:- Chain B: E.157
- Ligands: EDO.39
Ligand excluded by PLIPEDO.25: 3 residues within 4Å:- Chain B: H.102, E.157, D.158
Ligand excluded by PLIPEDO.26: 3 residues within 4Å:- Chain A: L.136, A.137
- Chain B: Q.103
Ligand excluded by PLIPEDO.27: 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.39: 6 residues within 4Å:- Chain A: P.222, A.223
- Chain B: P.176, G.177
- Chain C: E.111
- Ligands: EDO.24
Ligand excluded by PLIPEDO.41: 8 residues within 4Å:- Chain A: R.38, A.39, G.42, S.455, F.459
- Chain D: L.96, E.99, Y.104
Ligand excluded by PLIPEDO.42: 2 residues within 4Å:- Chain D: L.94, I.97
Ligand excluded by PLIPEDO.43: 4 residues within 4Å:- Chain E: Y.18, K.21, I.24, E.28
Ligand excluded by PLIPEDO.44: 2 residues within 4Å:- Chain E: R.53, R.57
Ligand excluded by PLIPEDO.45: 6 residues within 4Å:- Chain D: K.56
- Chain E: L.93, N.94, G.97, I.98, S.99
Ligand excluded by PLIPEDO.47: 7 residues within 4Å:- Chain A: T.489, T.490
- Chain F: S.67, T.68, V.69, W.71
- Ligands: EDO.14
Ligand excluded by PLIPEDO.48: 6 residues within 4Å:- Chain A: Y.510
- Chain F: P.36, K.37, T.39, N.47, L.48
Ligand excluded by PLIPEDO.49: 4 residues within 4Å:- Chain C: P.73, H.231
- Chain F: D.9, E.17
Ligand excluded by PLIPEDO.53: 6 residues within 4Å:- Chain C: G.120
- Chain G: A.46, F.47, I.48, L.53, R.54
Ligand excluded by PLIPEDO.54: 5 residues within 4Å:- Chain C: F.35
- Chain G: K.58, P.59, F.60, S.61
Ligand excluded by PLIPEDO.56: 3 residues within 4Å:- Chain C: P.13
- Chain L: H.2, Y.3
Ligand excluded by PLIPEDO.58: 2 residues within 4Å:- Chain M: S.20, F.23
Ligand excluded by PLIP- 5 x CHD: CHOLIC ACID(Non-covalent)
CHD.21: 7 residues within 4Å:- Chain A: M.271, G.272, W.275
- Chain B: Q.59, E.62, T.63, T.66
6 PLIP interactions:2 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:Q.59, B:E.62
- Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275
CHD.28: 9 residues within 4Å:- Chain A: H.233, W.288, D.300, T.301, Y.304
- Chain C: W.99, H.103
- Ligands: EDO.15, PGV.35
8 PLIP interactions:5 interactions with chain A, 3 interactions with chain C- Hydrophobic interactions: A:W.288, A:Y.304, C:W.99
- Hydrogen bonds: A:T.301, C:W.99
- Water bridges: A:T.301
- Salt bridges: A:H.233, C:H.103
CHD.33: 5 residues within 4Å:- Chain C: R.156, F.164, F.219, L.223
- Chain J: F.1
7 PLIP interactions:5 interactions with chain C, 2 interactions with chain J- Hydrophobic interactions: C:F.164, C:F.164, C:F.219, C:L.223, J:F.1
- Salt bridges: C:R.156
- Hydrogen bonds: J:F.1
CHD.51: 6 residues within 4Å:- Chain G: R.14, R.17, F.18, F.21, G.22
- Ligands: PEK.34
7 PLIP interactions:7 interactions with chain G- Hydrophobic interactions: G:F.18, G:F.18, G:F.21
- Water bridges: G:R.17, G:R.17
- Salt bridges: G:R.14, G:R.17
CHD.55: 8 residues within 4Å:- Chain A: I.3, L.7, F.8
- Chain J: Y.32, R.33, M.36, T.37, L.40
4 PLIP interactions:1 interactions with chain A, 3 interactions with chain J- Hydrophobic interactions: A:I.3, J:Y.32, J:R.33, J:M.36
- 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)
PSC.23: 19 residues within 4Å:- Chain A: F.321, L.324, H.328
- Chain B: L.37, I.41, M.45, H.52, M.56, D.57, V.61, I.64, W.65, L.68
- Chain E: H.5, E.6, D.40
- Chain I: L.13, A.14, L.17
12 PLIP interactions:2 interactions with chain A, 7 interactions with chain B, 3 interactions with chain I- Hydrophobic interactions: A:F.321, A:L.324, B:L.37, B:M.56, B:I.64, B:W.65, B:L.68, I:L.13, I:A.14
- Salt bridges: B:H.52, B:H.52
- Hydrogen bonds: I:A.14
- 4 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)
DMU.29: 11 residues within 4Å:- Chain A: L.110
- Chain C: S.29, M.33, F.37
- Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52
- Ligands: DMU.38
6 PLIP interactions:2 interactions with chain C, 1 interactions with chain A, 3 interactions with chain J- Hydrophobic interactions: C:M.33, C:F.37, A:L.110, J:L.50
- Hydrogen bonds: J:Y.45, J:Y.45
DMU.37: 6 residues within 4Å:- Chain C: W.116, P.117, V.254, W.258, W.259, S.261
7 PLIP interactions:7 interactions with chain C- Hydrophobic interactions: C:V.254, C:W.258, C:W.258
- Hydrogen bonds: C:W.116, C:W.259, C:S.261
- Water bridges: C:S.261
DMU.38: 11 residues within 4Å:- Chain C: M.33, N.38, S.39, T.41, I.45
- Chain J: T.37, L.38, G.41, G.42, Y.45
- Ligands: DMU.29
11 PLIP interactions:5 interactions with chain J, 6 interactions with chain C- Hydrophobic interactions: J:L.38, J:Y.45, J:Y.45, C:I.45
- Hydrogen bonds: J:Y.45, J:Y.45, C:N.38, C:N.38, C:S.39, C:S.39
- Water bridges: C:N.38
DMU.57: 12 residues within 4Å:- Chain A: F.459
- Chain D: W.98, Y.102
- Chain L: F.37
- Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36
8 PLIP interactions:4 interactions with chain M, 2 interactions with chain D, 1 interactions with chain A, 1 interactions with chain L- Hydrophobic interactions: M:L.27, M:A.30, M:L.34, D:W.98, D:W.98, A:F.459, L:F.37
- Water bridges: M:H.36
- 1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)
- 1 x CDL: CARDIOLIPIN(Non-covalent)
CDL.32: 25 residues within 4Å:- Chain C: T.48, M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, V.171, T.174, I.209, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226
- Chain J: K.8, F.12, L.31
- Ligands: PGV.31
27 PLIP interactions:22 interactions with chain C, 5 interactions with chain J- Hydrophobic interactions: C:M.51, C:M.54, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:V.171, C:T.174, C:I.209, C:T.213, C:I.216, C:I.216, C:V.217, C:F.220, J:L.31
- Hydrogen bonds: C:R.59, C:R.63
- Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8, J:K.8
- Water bridges: J:D.28
- 4 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.34: 13 residues within 4Å:- Chain C: K.157, H.158, Q.161, I.165, T.168, Y.172
- Chain F: A.1
- Chain G: R.17, F.21, G.22, L.23, P.26
- Ligands: CHD.51
12 PLIP interactions:7 interactions with chain G, 5 interactions with chain C- Hydrophobic interactions: G:F.21, G:F.21, G:L.23, G:P.26, C:I.165, C:Y.172
- Hydrogen bonds: G:R.17, C:K.157, C:H.158, C:Q.161
- Salt bridges: G:R.17, G:R.17
PEK.36: 9 residues within 4Å:- Chain C: Y.81, I.84, V.91, T.95, F.98, W.240, F.244, V.247, F.251
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:Y.81, C:I.84, C:V.91, C:F.98, C:F.98, C:W.240, C:W.240, C:W.240, C:V.247, C:F.251, C:F.251
- Hydrogen bonds: C:W.240
PEK.50: 23 residues within 4Å:- Chain A: H.151, V.155, I.158, A.203, L.210, L.215
- Chain C: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203
- Chain G: W.62, T.68, F.69, F.70, H.71, N.76
- Ligands: PGV.9
17 PLIP interactions:8 interactions with chain G, 5 interactions with chain A, 4 interactions with chain C- Hydrophobic interactions: G:F.69, G:F.70, A:V.155, A:I.158, A:L.210, A:L.215, A:L.215, C:W.34, C:I.188, C:F.203
- Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:I.188
- Water bridges: G:F.69, G:F.69
PEK.52: 4 residues within 4Å:- Chain G: S.2, G.6, D.7, T.11
No protein-ligand interaction detected (PLIP)- 1 x ZN: ZINC ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shimada, A. et al., X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem. (2018)
- Release Date
- 2018-08-15
- 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
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
M - Membrane
-
We predict this structure to be a membrane protein.
SMTL ID : 5zcp.1 (1 other biounit)
azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20 mM azide solution for 2 days
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 | 5b1b.2 | 5b3s.1 | 5b3s.2 | 5gpn.49 | 5gpn.50 | 5gpn.51 | 5gpn.53 | 5gpn.54 | 5gpn.55 | 5gpn.56 | 5gpn.57 | 5gpn.58 | 5gpn.59 | 5gpn.60 | 5gup.1 | 5gup.68 | 5gup.69 | 5gup.70 | 5gup.71 | 5gup.72 | 5gup.73 | 5gup.75 | 5gup.76 | 5gup.77 | 5gup.79 | 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.48 | 5xth.50 | 5xth.51 | 5xth.54 | 5xth.57 | 5xti.46 | 5xti.47 | 5xti.48 | 5xti.50 | 5xti.51 | 5xti.54 | 5xti.57 | 5xti.126 | 5xti.127 | 5xti.128 | 5xti.130 | 5xti.131 | 5xti.134 | 5xti.137 | 5z84.1 | 5z84.2 | 5z85.1 | 5z85.2 | 5z86.1 | 5z86.2 | 5zco.1 | 5zco.2 | 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 | 7dgr.69 | 7dgs.67 | 7dgs.68 | 7dgs.69 | 7dkf.68 | 7dkf.69 | 7dkf.70 | 7ev7.1 | 7ev7.2 | 7o37.1 | 7o3c.1 | 7o3e.1 | 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