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Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/ASU, with bound NADH

X-ray diffraction
3.1Å resolution
PDB entry 3iam coloured by chain, front view.
PDB entry 3iam coloured by chain, side view.
PDB entry 3iam coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Assembly composition:
hetero octamer (preferred)
Entry contents: 8 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: NADH-quinone oxidoreductase
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Multimeric state: hetero octamer
Accessible surface area: 81543.4 Å2
Buried surface area: 39363.55 Å2
Dissociation area: 4,676.11 Å2
Dissociation energy (ΔGdiss): 51.68 kcal/mol
Dissociation entropy (TΔSdiss): 14.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-176331
Assembly 2 (preferred)
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Assembly Name: NADH-quinone oxidoreductase
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Multimeric state: hetero octamer
Accessible surface area: 81575.51 Å2
Buried surface area: 39156.65 Å2
Dissociation area: 2,824.54 Å2
Dissociation energy (ΔGdiss): 26.71 kcal/mol
Dissociation entropy (TΔSdiss): 16.01 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-176331

Macromolecules

NADH-quinone oxidoreductase subunit 1
Chains: 1, A
Length: 438 amino acids
Theoretical weight: 48.69 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56222 (Residues: 1-438; Coverage: 100%)
Gene names: TTHA0089, nqo1
Pfam:
InterPro:
CATH:
NADH-quinone oxidoreductase subunit 1 in PDB entry 3iam, assembly 2, front view.
NADH-quinone oxidoreductase subunit 1 in PDB entry 3iam, assembly 2, side view.
NADH-quinone oxidoreductase subunit 1 in PDB entry 3iam, assembly 2, top view.
PDBe-KB: UniProt Coverage View: Q56222  
143850100150200250300350400
 
200400
UniProt
Q56222
Chains
Domains
Secondary structure
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Early folding residue predictions
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Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 2
Chains: 2, B
Length: 181 amino acids
Theoretical weight: 20.31 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56221 (Residues: 1-181; Coverage: 100%)
Gene names: TTHA0088, nqo2
Pfam: Thioredoxin-like [2Fe-2S] ferredoxin
InterPro:
CATH:
NADH-quinone oxidoreductase subunit 2 in PDB entry 3iam, assembly 2, front view.
NADH-quinone oxidoreductase subunit 2 in PDB entry 3iam, assembly 2, side view.
NADH-quinone oxidoreductase subunit 2 in PDB entry 3iam, assembly 2, top view.
PDBe-KB: UniProt Coverage View: Q56221  
118120406080100120140160180
 
50100150
UniProt
Q56221
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 3
Chains: 3, C
Length: 783 amino acids
Theoretical weight: 86.66 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56223 (Residues: 1-783; Coverage: 100%)
Gene names: TTHA0090, nqo3
Pfam:
InterPro:
NADH-quinone oxidoreductase subunit 3 in PDB entry 3iam, assembly 2, front view.
NADH-quinone oxidoreductase subunit 3 in PDB entry 3iam, assembly 2, side view.
NADH-quinone oxidoreductase subunit 3 in PDB entry 3iam, assembly 2, top view.
PDBe-KB: UniProt Coverage View: Q56223  
1783100200300400500600700
 
200400600
UniProt
Q56223
Chains
Domains
Secondary structure
Flexibility predictions
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NADH-quinone oxidoreductase subunit 4
Chains: 4, D
Length: 409 amino acids
Theoretical weight: 46.43 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56220 (Residues: 1-409; Coverage: 100%)
Gene names: TTHA0087, nqo4
Pfam: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
InterPro:
CATH: Cytochrome-c3 Hydrogenase, chain B
NADH-quinone oxidoreductase subunit 4 in PDB entry 3iam, assembly 2, front view.
NADH-quinone oxidoreductase subunit 4 in PDB entry 3iam, assembly 2, side view.
NADH-quinone oxidoreductase subunit 4 in PDB entry 3iam, assembly 2, top view.
PDBe-KB: UniProt Coverage View: Q56220  
140950100150200250300350400
 
100200300400
UniProt
Q56220
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 5
Chains: 5, E
Length: 207 amino acids
Theoretical weight: 23.89 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56219 (Residues: 1-207; Coverage: 100%)
Gene names: TTHA0086, nqo5
Pfam: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
InterPro:
NADH-quinone oxidoreductase subunit 5 in PDB entry 3iam, assembly 2, front view.
NADH-quinone oxidoreductase subunit 5 in PDB entry 3iam, assembly 2, side view.
NADH-quinone oxidoreductase subunit 5 in PDB entry 3iam, assembly 2, top view.
PDBe-KB: UniProt Coverage View: Q56219  
120720406080100120140160180200
 
50100150200
UniProt
Q56219
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 6
Chains: 6, F
Length: 181 amino acids
Theoretical weight: 20.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56218 (Residues: 1-181; Coverage: 100%)
Gene names: TTHA0085, nqo6
Pfam: NADH ubiquinone oxidoreductase, 20 Kd subunit
InterPro:
CATH: Rossmann fold
NADH-quinone oxidoreductase subunit 6 in PDB entry 3iam, assembly 2, front view.
NADH-quinone oxidoreductase subunit 6 in PDB entry 3iam, assembly 2, side view.
NADH-quinone oxidoreductase subunit 6 in PDB entry 3iam, assembly 2, top view.
PDBe-KB: UniProt Coverage View: Q56218  
118120406080100120140160180
 
50100150
UniProt
Q56218
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 9
Chains: 9, G
Length: 182 amino acids
Theoretical weight: 20.11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56224 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA0092, nqo9
Pfam: 4Fe-4S binding domain
InterPro:
CATH: Alpha-Beta Plaits
NADH-quinone oxidoreductase subunit 9 in PDB entry 3iam, assembly 2, front view.
NADH-quinone oxidoreductase subunit 9 in PDB entry 3iam, assembly 2, side view.
NADH-quinone oxidoreductase subunit 9 in PDB entry 3iam, assembly 2, top view.
PDBe-KB: UniProt Coverage View: Q56224  
118220406080100120140160180
 
50100150
UniProt
Q56224
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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NADH-quinone oxidoreductase subunit 15
Chains: 7, H
Length: 129 amino acids
Theoretical weight: 14.81 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKZ7 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA0496, nqo15
Pfam: NADH-quinone oxidoreductase chain 15
InterPro:
CATH: NADH-quinone oxidoreductase, subunit 15
NADH-quinone oxidoreductase subunit 15 in PDB entry 3iam, assembly 2, front view.
NADH-quinone oxidoreductase subunit 15 in PDB entry 3iam, assembly 2, side view.
NADH-quinone oxidoreductase subunit 15 in PDB entry 3iam, assembly 2, top view.
PDBe-KB: UniProt Coverage View: Q5SKZ7  
1129102030405060708090100110120
 
50100
UniProt
Q5SKZ7
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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