SMTL ID : 5z62.1

Structure of human cytochrome c oxidase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

3 x CU: COPPER (II) ION(Non-covalent)

CU.1: 3 residues within 4Å: Chain A: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.6: 7 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 Ligands: CU.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.200 CU.7: 7 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 Ligands: CU.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.196, B:C.200, B:H.204

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.198 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.198, A:H.368, A:D.369

2 x HEA: HEME-A(Non-covalent)

HEA.3: 34 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, I.73, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, F.425, Q.428, R.438, R.439, S.461, V.465, M.468 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:A.24, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:V.374, A:F.377, A:F.377, A:L.381, A:V.386, A:V.386, A:I.389, A:F.393, A:V.465 Hydrogen bonds: A:R.38, A:Y.54, A:S.382, A:Q.428, A:R.439 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.378, A:H.378, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.4: 30 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, G.317, F.321, 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: P.69, L.73 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:I.247, A:T.309, A:F.321, A:T.349, A:I.356, A:F.377, A:F.377, A:V.380, A:L.381, B:P.69, B:L.73, B:L.73 Hydrogen bonds: A:Y.244 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.240, A:H.376 Metal complexes: A:H.376

3 x PEE: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.5: 18 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, V.155, L.159 Chain C: H.8, M.26, T.27, W.56, W.57, V.74, L.78, G.81, F.85 Ligands: PEE.8, PEE.9 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:T.27, C:W.56, C:F.85, C:F.85, A:F.94, A:V.155, A:L.159 Hydrogen bonds: C:H.8, C:W.56, A:R.96, A:M.97 Salt bridges: A:R.96 PEE.8: 23 residues within 4Å: Chain C: M.53, W.57, V.60, T.61, S.64, T.65, H.70, F.85, E.89, F.92, H.206, I.209, T.212, F.213, I.216, R.220, H.225, H.230, H.231, F.232, G.233 Ligands: PEE.5, PEE.9 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:W.57, C:W.57, C:W.57, C:W.57, C:W.57, C:F.85, C:F.92, C:I.209, C:I.209, C:F.213, C:F.213, C:I.216 Hydrogen bonds: C:H.230, C:G.233 Salt bridges: C:R.220, C:R.220, C:H.230 PEE.9: 18 residues within 4Å: Chain A: L.215 Chain C: Y.180, S.183, F.185, T.186, I.187, F.197, V.198, G.201, F.202, L.205 Chain G: W.53, T.59, L.60, F.61, N.67 Ligands: PEE.5, PEE.8 10 PLIP interactions: 4 interactions with chain G, 6 interactions with chain C Hydrophobic interactions: G:W.53, C:F.202, C:F.202, C:L.205 Hydrogen bonds: G:T.59, G:L.60, G:F.61, C:S.183, C:S.183, C:I.187

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.10: 21 residues within 4Å: Chain A: I.286, W.288, M.297, D.298, T.301, F.305 Chain C: F.91, F.97, W.98, Y.101, H.102, L.105, A.106, F.250 Chain N: A.27, T.28, L.31, L.34, A.35, N.38, D.40 22 PLIP interactions: 7 interactions with chain A, 6 interactions with chain N, 9 interactions with chain C Hydrophobic interactions: A:I.286, A:W.288, A:W.288, A:F.305, N:A.27, N:T.28, N:L.31, N:L.34, N:A.35, C:F.91, C:F.97, C:F.97, C:W.98, C:W.98, C:Y.101, C:F.250 Hydrogen bonds: A:D.298, A:T.301, N:N.38 Salt bridges: A:H.233, C:H.102, C:H.102

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain F: C.60, C.62, C.82, C.85, A.87 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zong, S. et al., Structure of the intact 14-subunit human cytochrome c oxidase. Cell Res. (2018)

Release Date

2019-02-27

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 6A1, mitochondrial: G
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A2, mitochondrial: J
Cytochrome c oxidase subunit 7B, mitochondrial: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8A, mitochondrial: M
Cytochrome c oxidase subunit NDUFA4: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Membrane

We predict this structure to be a membrane protein.
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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 6A1, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A2, mitochondrial

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8A, mitochondrial

Cytochrome c oxidase subunit NDUFA4

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