SMTL ID : 7atn.1

Cytochrome c oxidase structure in R-state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.403, D.404 Chain B: D.222, S.246, E.247 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.247, A:H.403, A:D.404, H2O.2

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

HEA.2: 33 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, 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:T.50, A:M.98, A:V.103, A:F.412, A:M.416, A:V.421, A:I.424, A:I.459, A:I.459, A:F.460, A:F.500, A:F.500, A:F.500, A:F.503 Hydrogen bonds: A:T.50, A:T.50, A:I.91, A:W.164, A:Y.406, A:Q.463, A:R.474, A:Y.475 Water bridges: A:R.473, A:R.473 Salt bridges: A:R.473, A:R.474 pi-Stacking: A:F.412, A:H.413, A:F.460 Metal complexes: A:H.94 HEA.5: 30 residues within 4Å: Chain A: W.164, W.272, V.279, Y.280, I.282, I.283, H.325, H.326, I.347, T.351, G.352, V.355, F.383, T.384, 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: V.74, V.78 Ligands: CU.3 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.164, A:W.272, A:V.279, A:V.279, A:V.279, A:I.282, A:T.351, A:V.355, A:F.383, A:T.384, A:L.393, A:F.412, A:F.412, A:V.415, B:V.74, B:V.78 Hydrogen bonds: A:Y.280, A:Y.280 Water bridges: A:H.326, A:H.403, A:D.404, A:R.473, A:R.474 Salt bridges: A:H.403, A:R.473 pi-Cation interactions: A:H.276, A:H.276 Metal complexes: A:H.411

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

CU.3: 4 residues within 4Å: Chain A: H.276, H.325, H.326 Ligands: HEA.5 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.4: 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 CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.6: 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 PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.7: 19 residues within 4Å: Chain C: W.67, V.70, V.71, G.74, E.75, H.79, L.87, F.91, F.94, I.223, F.227, R.234, Q.239, M.240, T.241, Q.244, H.245, V.246, G.247 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:W.67, C:W.67, C:F.91, C:F.94, C:F.94, C:I.223, C:F.227, C:F.227, C:F.227, C:V.246 Hydrogen bonds: C:Q.244, C:Q.244, C:V.246, C:G.247 Salt bridges: C:E.75, C:H.79, C:R.234, C:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolbe, F. et al., Cytochrome c oxidase structure in R-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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