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Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-bound Fully Reduced State at 100 K

X-ray diffraction
1.8Å resolution
PDB entry 3ag3 coloured by chain, front view.
PDB entry 3ag3 coloured by chain, side view.
PDB entry 3ag3 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: 61577.74 Å2
Buried surface area: 80861.1 Å2
Dissociation area: 1,602.4 Å2
Dissociation energy (ΔGdiss): 7.8 kcal/mol
Dissociation entropy (TΔSdiss): 12.06 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132466
Assembly 2
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Assembly Name: Respiratory chain complex IV
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Multimeric state: hetero tridecamer
Accessible surface area: 61527.18 Å2
Buried surface area: 80905.38 Å2
Dissociation area: 1,003.26 Å2
Dissociation energy (ΔGdiss): 17.7 kcal/mol
Dissociation entropy (TΔSdiss): 8.3 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132466

Macromolecules

Cytochrome c oxidase subunit 1
Chains: A, N
Length: 514 amino acids
Theoretical weight: 57.09 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00396 (Residues: 1-514; Coverage: 100%)
Gene names: COI, COXI, MT-CO1, MTCO1
Pfam: Cytochrome C and Quinol oxidase polypeptide I
InterPro:
CATH: Cytochrome c oxidase-like, subunit I domain
Cytochrome c oxidase subunit 1 in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 1 in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 1 in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 2
Chains: B, 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:
CATH:
Cytochrome c oxidase subunit 2 in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 2 in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 2 in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 3
Chains: C, P
Length: 261 amino acids
Theoretical weight: 29.96 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00415 (Residues: 1-261; Coverage: 100%)
Gene names: COIII, COXIII, MT-CO3, MTCO3
Pfam: Cytochrome c oxidase subunit III
InterPro:
CATH:
Cytochrome c oxidase subunit 3 in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 3 in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 3 in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Chains: D, Q
Length: 147 amino acids
Theoretical weight: 17.18 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00423 (Residues: 23-169; Coverage: 87%)
Gene names: COX4, COX4I1
Pfam: Cytochrome c oxidase subunit IV
InterPro:
CATH: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 5A, mitochondrial
Chains: E, R
Length: 109 amino acids
Theoretical weight: 12.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00426 (Residues: 44-152; Coverage: 72%)
Gene name: COX5A
Pfam: Cytochrome c oxidase subunit Va
InterPro:
CATH: Cytochrome c oxidase, subunit Va/VI
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 5B, mitochondrial
Chains: F, S
Length: 98 amino acids
Theoretical weight: 10.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00428 (Residues: 32-129; Coverage: 76%)
Gene name: COX5B
Pfam: Cytochrome c oxidase subunit Vb
InterPro:
CATH: Cytochrome c oxidase, subunit Vb
Cytochrome c oxidase subunit 5B, mitochondrial in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 5B, mitochondrial in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 5B, mitochondrial in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 6A2, mitochondrial
Chains: G, T
Length: 85 amino acids
Theoretical weight: 9.63 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07471 (Residues: 13-97; Coverage: 88%)
Gene names: COX6A, COX6A2
Pfam: Cytochrome c oxidase subunit VIa
InterPro:
CATH: Cytochrome c oxidase, subunit VIa
Cytochrome c oxidase subunit 6A2, mitochondrial in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 6A2, mitochondrial in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 6A2, mitochondrial in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 6B1
Chains: H, U
Length: 85 amino acids
Theoretical weight: 10.04 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00429 (Residues: 2-86; Coverage: 99%)
Gene names: COX6B, COX6B1
Pfam: Cytochrome oxidase c subunit VIb
InterPro:
CATH: Cytochrome c oxidase, subunit VIb
Cytochrome c oxidase subunit 6B1 in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 6B1 in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 6B1 in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 6C
Chains: I, V
Length: 73 amino acids
Theoretical weight: 8.54 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P04038 (Residues: 2-74; Coverage: 99%)
Gene name: COX6C
Pfam: Cytochrome c oxidase subunit VIc
InterPro:
CATH: Mitochondrial cytochrome c oxidase subunit VIc/VIIs
Cytochrome c oxidase subunit 6C in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 6C in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 6C in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 7A1, mitochondrial
Chains: J, W
Length: 59 amino acids
Theoretical weight: 6.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07470 (Residues: 22-80; Coverage: 74%)
Gene names: COX7A, COX7A1, COX7AH
Pfam: Cytochrome c oxidase subunit VII
InterPro:
CATH: Cytochrome c oxidase, subunit VIIa
Cytochrome c oxidase subunit 7A1, mitochondrial in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 7A1, mitochondrial in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 7A1, mitochondrial in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 7B, mitochondrial
Chains: K, X
Length: 56 amino acids
Theoretical weight: 6.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13183 (Residues: 25-80; Coverage: 70%)
Gene name: COX7B
Pfam: Cytochrome C oxidase chain VIIB
InterPro:
CATH: Cytochrome C Oxidase, chain K
Cytochrome c oxidase subunit 7B, mitochondrial in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 7B, mitochondrial in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 7B, mitochondrial in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 7C, mitochondrial
Chains: L, Y
Length: 47 amino acids
Theoretical weight: 5.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00430 (Residues: 17-63; Coverage: 75%)
Gene names: COX7C, COX7CP1
Pfam: Cytochrome c oxidase subunit VIIc
InterPro:
CATH: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 7C, mitochondrial in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 7C, mitochondrial in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 7C, mitochondrial in PDB entry 3ag3, assembly 1, top view.
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Cytochrome c oxidase subunit 8B, mitochondrial
Chains: M, Z
Length: 46 amino acids
Theoretical weight: 4.97 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P10175 (Residues: 25-70; Coverage: 66%)
Gene names: COX8B, COX8H
Pfam: Cytochrome oxidase c subunit VIII
InterPro:
CATH: Cytochrome c oxidase, subunit 8
Cytochrome c oxidase subunit 8B, mitochondrial in PDB entry 3ag3, assembly 1, front view.
Cytochrome c oxidase subunit 8B, mitochondrial in PDB entry 3ag3, assembly 1, side view.
Cytochrome c oxidase subunit 8B, mitochondrial in PDB entry 3ag3, assembly 1, top view.
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