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Mammalian CIV with GDN bound

Electron Microscopy
3.1Å resolution
PDB entry 8d4t coloured by chain, front view.
PDB entry 8d4t coloured by chain, side view.
PDB entry 8d4t coloured by chain, top view.
Source organism: Bos taurus
Assembly composition:
hetero tridecamer (preferred)
Entry contents: 13 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Respiratory chain complex IV
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Multimeric state: hetero tridecamer
Accessible surface area: 59557.25 Å2
Buried surface area: 60822.26 Å2
Dissociation area: 1,503.34 Å2
Dissociation energy (ΔGdiss): 5.5 kcal/mol
Dissociation entropy (TΔSdiss): 12.11 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132468

Macromolecules

Cytochrome c oxidase subunit 1
Chain: N
Length: 513 amino acids
Theoretical weight: 56.96 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00396 (Residues: 1-513; Coverage: 100%)
Gene names: COI, COXI, MT-CO1, MTCO1
Pfam: Cytochrome C and Quinol oxidase polypeptide I
InterPro:
Cytochrome c oxidase subunit 1 in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 1 in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 1 in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 2
Chain: O
Length: 227 amino acids
Theoretical weight: 26.07 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P68530 (Residues: 1-227; Coverage: 100%)
Gene names: COII, COX2, COXII, MT-CO2, MTCO2
Pfam:
InterPro:
Cytochrome c oxidase subunit 2 in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 2 in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 2 in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 3
Chain: P
Length: 258 amino acids
Theoretical weight: 29.59 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00415 (Residues: 4-261; Coverage: 99%)
Gene names: COIII, COXIII, MT-CO3, MTCO3
Pfam: Cytochrome c oxidase subunit III
InterPro:
Cytochrome c oxidase subunit 3 in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 3 in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 3 in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Chain: Q
Length: 137 amino acids
Theoretical weight: 16.15 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00423 (Residues: 32-168; Coverage: 81%)
Gene names: COX4, COX4I1
Pfam: Cytochrome c oxidase subunit IV
InterPro:
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 5A, mitochondrial
Chain: R
Length: 102 amino acids
Theoretical weight: 11.72 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00426 (Residues: 49-150; Coverage: 67%)
Gene name: COX5A
Pfam: Cytochrome c oxidase subunit Va
InterPro:
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 5B, mitochondrial
Chain: S
Length: 91 amino acids
Theoretical weight: 10.02 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00428 (Residues: 35-125; Coverage: 71%)
Gene name: COX5B
Pfam: Cytochrome c oxidase subunit Vb
InterPro:
Cytochrome c oxidase subunit 5B, mitochondrial in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 5B, mitochondrial in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 5B, mitochondrial in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 6A2, mitochondrial
Chain: T
Length: 72 amino acids
Theoretical weight: 8.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07471 (Residues: 24-95; Coverage: 74%)
Gene names: COX6A, COX6A2
Pfam: Cytochrome c oxidase subunit VIa
InterPro:
Cytochrome c oxidase subunit 6A2, mitochondrial in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 6A2, mitochondrial in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 6A2, mitochondrial in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 6B1
Chain: U
Length: 78 amino acids
Theoretical weight: 9.28 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00429 (Residues: 9-86; Coverage: 91%)
Gene names: COX6B, COX6B1
Pfam: Cytochrome oxidase c subunit VIb
InterPro:
Cytochrome c oxidase subunit 6B1 in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 6B1 in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 6B1 in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 6C
Chain: V
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P04038 (Residues: 5-74; Coverage: 95%)
Gene name: COX6C
Pfam: Cytochrome c oxidase subunit VIc
InterPro:
Cytochrome c oxidase subunit 6C in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 6C in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 6C in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 7A1, mitochondrial
Chain: W
Length: 55 amino acids
Theoretical weight: 6.19 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07470 (Residues: 22-76; Coverage: 69%)
Gene names: COX7A, COX7A1, COX7AH
Pfam: Cytochrome c oxidase subunit VII
InterPro:
Cytochrome c oxidase subunit 7A1, mitochondrial in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 7A1, mitochondrial in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 7A1, mitochondrial in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 7B, mitochondrial
Chain: X
Length: 47 amino acids
Theoretical weight: 5.27 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13183 (Residues: 32-78; Coverage: 59%)
Gene name: COX7B
Pfam: Cytochrome C oxidase chain VIIB
InterPro:
Cytochrome c oxidase subunit 7B, mitochondrial in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 7B, mitochondrial in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 7B, mitochondrial in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 7C, mitochondrial
Chain: Y
Length: 46 amino acids
Theoretical weight: 5.36 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00430 (Residues: 18-63; Coverage: 73%)
Gene names: COX7C, COX7CP1
Pfam: Cytochrome c oxidase subunit VIIc
InterPro:
Cytochrome c oxidase subunit 7C, mitochondrial in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 7C, mitochondrial in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 7C, mitochondrial in PDB entry 8d4t, assembly 1, top view.
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Cytochrome c oxidase subunit 8A, mitochondrial
Chain: M
Length: 43 amino acids
Theoretical weight: 4.77 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P10176 (Residues: 26-68; Coverage: 62%)
Gene names: COX8, COX8A, COX8L
Pfam: Cytochrome oxidase c subunit VIII
InterPro:
Cytochrome c oxidase subunit 8A, mitochondrial in PDB entry 8d4t, assembly 1, front view.
Cytochrome c oxidase subunit 8A, mitochondrial in PDB entry 8d4t, assembly 1, side view.
Cytochrome c oxidase subunit 8A, mitochondrial in PDB entry 8d4t, assembly 1, top view.
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