SMTL ID : 7z10.1

Monomeric respiratory complex IV isolated from S. cerevisiae

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.241, H.290, H.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.241, A:H.290, A:H.291

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

HEA.2: 32 residues within 4Å: Chain A: F.19, I.23, G.26, T.30, S.33, I.36, R.37, V.59, H.62, A.63, M.66, I.67, V.71, W.127, Y.371, V.374, F.377, H.378, L.381, S.382, I.386, L.389, F.390, I.424, F.425, M.428, R.438, R.439, S.458, A.461, L.465, F.468 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:F.19, A:I.23, A:I.36, A:V.59, A:A.63, A:M.66, A:I.67, A:V.71, A:Y.371, A:V.374, A:F.377, A:L.381, A:L.381, A:I.386, A:I.386, A:I.386, A:L.389, A:L.389, A:F.390, A:F.390, A:I.424, A:F.425, A:L.465, A:L.465, A:F.468 Hydrogen bonds: A:R.439 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.377, A:H.378 Metal complexes: A:H.62 HEA.3: 33 residues within 4Å: Chain A: W.127, W.237, V.244, Y.245, I.248, H.290, H.291, T.309, I.312, A.313, T.316, G.317, I.320, F.321, T.349, G.352, L.353, G.355, V.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.35, P.74, I.77, L.78 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.237, A:V.244, A:V.244, A:Y.245, A:I.248, A:T.316, A:I.320, A:F.321, A:T.349, A:L.353, A:V.356, A:L.358, A:A.359, A:F.377, A:F.377, A:V.380, A:L.381, B:I.35, B:I.35, B:P.74, B:I.77 Hydrogen bonds: A:Y.245, A:Y.245, A:R.438 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.241 Metal complexes: A:H.376

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.208 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.208, A:H.368, A:D.369

3 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.5: 13 residues within 4Å: Chain A: F.95, P.96, R.97, I.98, L.160 Chain C: H.15, W.65, F.66, I.69, H.79, I.87, F.94 Ligands: PEF.8 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.160, C:W.65, C:W.65, C:F.94 Hydrogen bonds: A:R.97, A:I.98, C:H.15, C:H.79 Salt bridges: A:R.97 PEF.6: 13 residues within 4Å: Chain A: V.16, L.17, F.19, M.20, I.23, I.400, L.472 Chain H: P.12, F.13, R.18, H.26, F.29, F.30 13 PLIP interactions: 7 interactions with chain H, 6 interactions with chain A Hydrophobic interactions: H:F.13, H:F.13, H:F.29, H:F.29, H:F.30, A:V.16, A:F.19, A:F.19, A:I.23, A:I.400, A:L.472 Hydrogen bonds: H:S.25 Salt bridges: H:R.18 PEF.8: 18 residues within 4Å: Chain C: F.66, I.69, V.70, A.73, T.74, I.87, F.91, M.218, M.222, V.225, R.229, H.234, T.236, H.239, V.241, G.242 Chain D: E.35 Ligands: PEF.5 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:I.87, C:F.91, C:V.225 Hydrogen bonds: C:H.239, C:V.241, C:G.242 Salt bridges: C:R.229, C:R.229

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

CUA.7: 6 residues within 4Å: Chain B: H.171, C.206, E.208, C.210, H.214, M.217 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.171, B:C.206, B:C.206, B:E.208, B:C.210, B:C.210, B:H.214

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 6 residues within 4Å: Chain D: C.83, G.85, H.91, C.106, C.109, S.111 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.83, D:H.91, D:C.106, D:C.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ing, G. et al., Cryo-EM structure of a monomeric yeast S. cerevisiae complex IV isolated with maltosides: Implications in supercomplex formation. Biochim Biophys Acta Bioenerg (2022)

Release Date

2022-08-03

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3: C
Cytochrome c oxidase subunit 4, mitochondrial: D
Cytochrome c oxidase polypeptide 5A, mitochondrial: E
Cytochrome c oxidase subunit 6, mitochondrial: F
CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7: G
Cytochrome c oxidase polypeptide VIII, mitochondrial: H
CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9: I

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

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; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3

Cytochrome c oxidase subunit 4, mitochondrial

Cytochrome c oxidase polypeptide 5A, mitochondrial

Cytochrome c oxidase subunit 6, mitochondrial

CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7

Cytochrome c oxidase polypeptide VIII, mitochondrial

CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9

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