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MolNFT v1 · #183672 · protein

Respiratory complex I from escherichia COLI - focused refinement of cytoplasmic arm

7NZ1 · NADH-quinone oxidoreductase subunit B: “Respiratory complex I from escherichia COLI - focused refinement of cytoplasmic arm”. Electron microscopy, 4 ligands (SF4, FES, FMN), 20 pockets (best druggability 0.83). MolNFT v1 #183672 on…

PDB
7NZ1
Type
protein
Length
2,361 residues
Chains
6
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
NADH-quinone oxidoreductase subunit B; NADH-quinone oxidoreductase subunit C/D…
EC
7.1.1.2
UniProt
P33599, P0AFD1, P31979, P33602, P0AFD6
Ligands
SF4, FES, FMN, CA
Pockets
20 · best druggability 0.83

Structure

electron microscopy · 6 distinct chains · 35% helix, 16% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BNADH-quinone oxidoreductase subunit B (EC 7.1.1.2)protein14034% helix, 13% strand—
DNADH-quinone oxidoreductase subunit C/D (EC 7.1.1.2)protein57540% helix, 15% strandP33599
ENADH-quinone oxidoreductase subunit E (EC 7.1.1.2)protein15647% helix, 12% strandP0AFD1
FNADH-quinone oxidoreductase subunit F (EC 7.1.1.2)protein44141% helix, 13% strandP31979
GNADH-quinone oxidoreductase subunit G (EC 7.1.1.2)protein90731% helix, 19% strandP33602
INADH-quinone oxidoreductase subunit I (EC 7.1.1.2)protein14215% helix, 23% strandP0AFD6

Ligands and binding sites

  • SF4 · Iron/sulfur cluster · ligand · 7 copies · chains B, D, F, G, I
  • FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, F, G
  • FMN · Flavin mononucleotide · ligand · chains F
  • CA · Calcium ion · metal · chains G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
18220.830.8567empty
21590.810.9733empty
310700.810.82101empty
41220.790.9836empty
59690.770.79112empty

Interfaces

13 interfaces between chains.

  • E–F · 2002 Ų buried · 26 hydrogen bonds · protein-protein
  • B–I · 1954 Ų buried · 34 hydrogen bonds · protein-protein
  • D–G · 1948 Ų buried · 25 hydrogen bonds · protein-protein
  • B–D · 1928 Ų buried · 15 hydrogen bonds · protein-protein
  • G–I · 1897 Ų buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (oxidation).

Compared structures

  • 7NZ1 · Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm · the same entry in another collection · chain I against I, TM-score 1.00
  • P33602 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit G (P33602) · a predicted model of the same protein · chain G against A, TM-score 0.99
  • P33599 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit C/D (P33599) · a predicted model of the same protein · chain D against A, TM-score 0.97
  • P0AFD1 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit E (P0AFD1) · a predicted model of the same protein · chain E against A, TM-score 0.97
  • P31979 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit F (P31979) · a predicted model of the same protein · chain F against A, TM-score 0.96
  • P0AFD6 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit I (P0AFD6) · a predicted model of the same protein · chain I against A, TM-score 0.90

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