SMTL ID : 8c8q.1

Cytochrome c oxidase from Schizosaccharomyces pombe

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEA.1: 21 residues within 4Å: Chain A: L.29, S.39, R.43, Y.61, H.68, M.72, I.77, G.132, W.133, F.384, H.385, S.389, L.393, L.396, Y.400, V.428, R.445, R.446, S.465, S.468, F.475 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:I.77, A:F.384, A:F.384, A:L.393, A:L.396, A:Y.400, A:V.428, A:F.475 Hydrogen bonds: A:S.39, A:S.39, A:R.43, A:W.133, A:R.446 Salt bridges: A:R.445, A:R.446 pi-Stacking: A:H.68, A:F.384, A:H.385 Metal complexes: A:H.68, A:H.385 HEA.2: 28 residues within 4Å: Chain A: W.133, W.243, V.250, Y.251, I.254, H.296, T.315, I.318, A.319, T.322, G.323, T.356, G.359, L.360, G.362, V.363, L.365, S.366, D.371, H.375, V.380, H.383, F.384, V.387, L.388, R.445 Chain B: I.44, I.88 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.243, A:V.250, A:V.250, A:I.254, A:T.315, A:T.322, A:V.363, A:L.365, A:V.380, A:F.384, A:F.384, A:V.387, A:L.388, A:L.388, B:I.44, B:I.88 Hydrogen bonds: A:Y.251, A:Y.251 Salt bridges: A:H.375, A:R.445 pi-Cation interactions: A:H.247 Metal complexes: A:H.383

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

CU.3: 3 residues within 4Å: Chain A: H.247, H.296, H.297 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.247, A:H.296, A:H.297

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: H.375, D.376 Chain B: D.194, E.219 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.376, B:E.219

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: E.45, A.48, G.50, P.448 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.48, A:G.50, A:P.448

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

PEF.6: 18 residues within 4Å: Chain A: Y.101, P.102, R.103, V.104, I.162, A.210 Chain C: H.13, L.24, L.28, W.63, F.64, H.77, L.85, G.88, F.89, F.92 Ligands: PEF.9, PEF.10 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:I.162, A:A.210, C:L.24, C:L.28, C:W.63, C:F.64, C:F.92, C:F.92 Salt bridges: A:R.103 Hydrogen bonds: C:E.70, C:E.70 PEF.7: 11 residues within 4Å: Chain B: G.47, V.48, T.71, H.73, I.80, W.81, I.84, P.85 Chain I: K.11, I.14, F.18 7 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F, 2 interactions with chain I Hydrophobic interactions: B:V.48, B:I.80, B:I.84, B:P.85, I:I.14, I:F.18 Hydrogen bonds: F:H.40 PEF.9: 17 residues within 4Å: Chain C: M.60, F.64, M.67, N.72, H.77, L.85, H.215, V.218, I.221, L.222, L.235, H.239, H.240, N.241, G.242, C.245 Ligands: PEF.6 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.64, C:F.64, C:F.64, C:I.221, C:L.222 Hydrogen bonds: C:H.77, C:H.234, C:H.239, C:N.241, C:G.242 Salt bridges: C:H.239 PEF.10: 18 residues within 4Å: Chain A: L.159, F.214 Chain C: C.32, A.35, Y.189, A.192, T.195, I.196, Y.206, F.207, L.211 Chain K: W.109, T.115, L.116, F.117, W.118, N.123 Ligands: PEF.6 14 PLIP interactions: 5 interactions with chain K, 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: K:W.109, A:L.159, A:F.214, A:F.214, A:F.214, C:A.35, C:F.207, C:L.211 Hydrogen bonds: K:T.115, K:L.116, K:F.117, K:F.117, C:Y.189, C:I.196

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

CUA.8: 7 residues within 4Å: Chain B: H.182, C.217, E.219, L.220, C.221, H.225, M.228 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.182, B:E.219, B:C.221, B:H.225

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain D: C.120, H.128, C.143, C.146 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.120, D:H.128, D:C.143, D:C.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moe, A. et al., Cryo-EM structure and function of S. pombe complex IV with bound respiratory supercomplex factor. Commun Chem (2023)

Release Date

2023-03-01

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4, mitochondrial: D
Cytochrome c oxidase polypeptide 5, mitochondrial: E
Cytochrome c oxidase subunit 6, mitochondrial: F
Cytochrome c oxidase subunit 7: G
Cytochrome c oxidase polypeptide VIII, mitochondrial: H
Cytochrome c oxidase subunit 9, mitochondrial: I
Cytochrome c oxidase subunit 12, mitochondrial: J
Cytochrome c oxidase subunit 13, mitochondrial: K
Respiratory supercomplex factor 2 homolog C1565.01: L
Unknown polypeptide: M

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

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, mitochondrial

Cytochrome c oxidase polypeptide 5, mitochondrial

Cytochrome c oxidase subunit 6, mitochondrial

Cytochrome c oxidase subunit 7

Cytochrome c oxidase polypeptide VIII, mitochondrial

Cytochrome c oxidase subunit 9, mitochondrial

Cytochrome c oxidase subunit 12, mitochondrial

Cytochrome c oxidase subunit 13, mitochondrial

Respiratory supercomplex factor 2 homolog C1565.01

Unknown polypeptide

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