SMTL ID : 7au3.1

Cytochrome c oxidase structure in F-state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.403, D.404 Chain B: D.222, E.247 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.403, A:D.404, B:E.247, H2O.3, H2O.6

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

HEA.2: 34 residues within 4Å: Chain A: L.36, G.40, V.47, T.50, M.53, R.54, W.87, I.91, H.94, G.95, M.98, M.99, V.102, V.103, G.163, W.164, Y.406, F.412, H.413, M.416, S.417, V.421, I.424, M.452, S.456, I.459, F.460, Q.463, R.473, R.474, Y.475, S.496, F.500, F.503 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:V.47, A:T.50, A:I.91, A:M.98, A:V.103, A:W.164, A:M.416, A:V.421, A:I.424, A:F.460, A:F.460, A:F.500, A:F.500, A:F.500, A:F.503 Hydrogen bonds: A:T.50, A:T.50, A:R.54, A:W.164, A:Y.406, A:Q.463, A:R.474, A:Y.475 Water bridges: A:R.473 Salt bridges: A:R.473, A:R.474 pi-Stacking: A:F.412, A:F.460 Metal complexes: A:H.94, A:H.413 HEA.3: 31 residues within 4Å: Chain A: W.164, W.272, V.279, Y.280, H.325, H.326, T.344, I.347, A.348, T.351, G.352, V.355, F.383, G.387, G.390, V.391, L.393, S.394, D.399, H.403, V.408, H.411, F.412, V.415, M.416, R.473 Chain B: P.114, I.117, L.118 Ligands: O.6, 2FK.7 31 PLIP interactions: 27 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.272, A:V.279, A:V.279, A:V.279, A:T.344, A:A.348, A:T.351, A:V.355, A:F.383, A:V.391, A:V.391, A:L.393, A:L.393, A:F.412, A:F.412, A:V.415, B:P.114, B:I.117, B:L.118 Hydrogen bonds: A:Y.280, A:D.399 Water bridges: A:H.326, A:D.404, A:D.404, A:R.473, A:R.473 Salt bridges: A:H.403, A:R.473 pi-Stacking: A:H.325 Metal complexes: A:H.411, O.6

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

CU.4: 5 residues within 4Å: Chain A: H.276, H.325, H.326 Ligands: O.6, 2FK.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.276, A:H.325, A:H.326

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: E.56, H.59, G.61, Q.63 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.56, A:E.56, A:H.59, A:G.61

1 x O: OXYGEN ATOM(Non-covalent)

O.6: 4 residues within 4Å: Chain A: H.411 Ligands: HEA.3, CU.4, 2FK.7 No protein-ligand interaction detected (PLIP)

1 x 2FK: SUPEROXO ION(Non-covalent)

2FK.7: 7 residues within 4Å: Chain A: W.272, G.275, V.279, H.326 Ligands: HEA.3, CU.4, O.6 No protein-ligand interaction detected (PLIP)

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.8: 6 residues within 4Å: Chain B: H.210, C.245, E.247, C.249, H.253, M.256 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.210, B:C.245, B:C.245, B:E.247, B:C.249, B:C.249, B:H.253

1 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.9: 29 residues within 4Å: Chain A: F.127, P.128, R.129, L.130, L.133, M.137, H.187, V.188, A.191, I.194, L.195, I.198, P.236 Chain C: Q.10, L.12, G.21, A.25, V.59, M.63, W.66, W.67, V.70, E.73, H.79, G.90, F.94, S.97, E.98, F.101 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:L.130, A:L.130, A:L.133, A:A.191, A:I.194, A:L.195, A:I.198, A:P.236, C:V.59, C:W.66, C:W.66, C:W.66, C:W.67, C:F.101 Hydrogen bonds: A:A.126, A:L.130, C:E.73 Salt bridges: A:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolbe, F. et al., Cytochrome c oxidase structure in F-state. To Be Published

Release Date

2021-12-01

Peptides

Cytochrome c oxidase subunit 1-beta: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1-beta

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4

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