MolNFT v1 · #92410 · protein
Crystal structure of ndh with quinone
4G74 · Rotenone-insensitive NADH-ubiquinone oxidoreductase…: “Crystal structure of ndh with quinone”. X-ray diffraction, 4 ligands (UQ5, TRT, FAD), 12 pockets (best druggability 0.80). MolNFT v1 #92410 on GenesisL1: 3D structure, binding…
- PDB
- 4G74
- Type
- protein
- Length
- 934 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
- EC
- 1.6.5.9
- UniProt
- P32340
- Ligands
- UQ5, TRT, FAD, MG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (EC 1.6.5.9) | protein | 471 | 34% helix, 26% strand | P32340 |
| B | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (EC 1.6.5.9) | protein | 463 | 35% helix, 27% strand | P32340 |
Ligands and binding sites
- UQ5 · 2,3-dimethoxy-5-methyl-6-(3,11,15,19-tetramethyl-eicosa-2,6,10,14,18-pentaenyl)-[1,4]benzoquinone · ligand · 4 copies · chains A, B
- TRT · Fragment of triton X-100 · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.80 | 0.82 | 83 | UQ5, FAD, MG |
| 2 | 306 | 0.80 | 0.91 | 37 | empty |
| 3 | 290 | 0.80 | 0.91 | 34 | empty |
| 4 | 853 | 0.79 | 0.82 | 73 | UQ5, FAD, MG |
| 5 | 88 | 0.73 | 0.96 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2129 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P32340
- Elsewhere: RCSB PDB 4G74 · PDBe 4G74 · UniProt P32340
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