SMTL ID : 7au6.1

Cytochrome c oxidase structure in O-state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

HEA.1: 37 residues within 4Å: Chain A: L.36, G.40, G.43, V.47, T.50, M.53, R.54, W.87, I.91, T.92, H.94, G.95, M.98, M.99, V.102, V.103, A.106, 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 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: A:L.36, A:V.47, A:T.50, A:I.91, A:M.98, A:V.102, A:V.103, A:A.106, A:F.412, A:M.416, A:V.421, A:V.421, A:I.424, A:I.459, A:F.460, A:F.460, A:F.500, A:F.500, A:F.500, A:F.500, A:F.503 Hydrogen bonds: A:T.50, A:T.50, A:R.54, A:I.91, 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.2: 28 residues within 4Å: Chain A: W.164, W.272, V.279, Y.280, H.325, H.326, T.344, I.347, T.351, G.352, V.355, F.356, 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 Ligands: OXY.5, PEO.11 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:W.272, A:V.279, A:V.279, A:V.279, A:T.344, A:T.351, A:V.355, A:F.356, A:T.384, A:V.391, A:L.393, A:L.393, A:V.408, A:F.412, A:F.412, A:V.415 Hydrogen bonds: A:Y.280, A:D.399 Water bridges: A:Y.280, A:D.404, A:R.473, A:R.474 Salt bridges: A:H.403, A:R.473, A:R.474 Metal complexes: A:H.411

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

CU.3: 5 residues within 4Å: Chain A: H.276, H.325, H.326 Ligands: OXY.5, PEO.11 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 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.56, A:H.59, A:G.61, H2O.1, H2O.3

6 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 6 residues within 4Å: Chain A: W.272, V.279, H.326 Ligands: HEA.2, CU.3, PEO.11 No protein-ligand interaction detected (PLIP) OXY.6: 3 residues within 4Å: Chain A: Y.93, V.96, A.182 No protein-ligand interaction detected (PLIP) OXY.7: 5 residues within 4Å: Chain A: Y.93, L.97, G.145, V.146, L.149 No protein-ligand interaction detected (PLIP) OXY.8: 4 residues within 4Å: Chain A: V.42, I.45, L.97, V.146 No protein-ligand interaction detected (PLIP) OXY.9: 4 residues within 4Å: Chain A: V.96, F.100, W.164, V.186 No protein-ligand interaction detected (PLIP) OXY.10: 5 residues within 4Å: Chain A: F.100, W.164, V.165, L.271, F.274 No protein-ligand interaction detected (PLIP)

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.11: 6 residues within 4Å: Chain A: H.276, H.325, H.326 Ligands: HEA.2, CU.3, OXY.5 No protein-ligand interaction detected (PLIP)

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

MN.12: 5 residues within 4Å: Chain A: H.403, D.404 Chain B: D.222, S.246, E.247 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.247, A:D.404, H2O.4, H2O.5, H2O.6

1 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.13: 6 residues within 4Å: Chain B: H.210, C.245, E.247, C.249, H.253, M.256 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:H.210, B:C.245, B:C.245, B:E.247, B:C.249, B:H.253

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.14: 15 residues within 4Å: Chain A: H.269, F.273, W.323, Q.336 Chain C: M.100, V.103, F.106, W.107, I.110, K.111, Y.115, P.122, D.125 Chain D: S.38, L.42 12 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: D:L.42, A:F.273, A:F.273, C:V.103, C:F.106, C:W.107, C:I.110, C:I.110 Hydrogen bonds: A:Q.336 Salt bridges: A:H.269, C:D.125 pi-Cation interactions: C:Y.115 PC1.15: 21 residues within 4Å: Chain C: L.56, L.60, W.67, V.70, V.71, G.74, E.75, H.79, L.87, F.94, I.223, F.227, V.230, R.234, Q.239, M.240, T.241, Q.244, H.245, V.246, G.247 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:L.56, C:L.60, C:W.67, C:W.67, C:W.67, C:W.67, C:W.67, C:V.70, C:F.94, C:I.223, C:F.227, C:F.227, C:F.227, C:V.230, C:V.246 Hydrogen bonds: C:V.246, C:G.247 Salt bridges: C:E.75, C:H.79, C:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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