Research workbench
Crystal structure of nqrf FAD-binding domain from vibrio cholerae
Analyse Crystal structure of nqrf FAD-binding domain from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U9U
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Na(+)-translocating NADH-quinone reductase subunit F
- EC
- 1.6.5.-
- UniProt
- Q9X4Q8
- Ligands
- FAD, MG, NA
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Na(+)-translocating NADH-quinone reductase subunit F (EC 1.6.5.-) | protein | 279 | 31% helix, 31% strand | Q9X4Q8 |
| B | Na(+)-translocating NADH-quinone reductase subunit F (EC 1.6.5.-) | protein | 278 | 31% helix, 31% strand | Q9X4Q8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.83 | 0.84 | 99 | empty |
| 2 | 508 | 0.65 | 0.77 | 65 | FAD, ACT |
| 3 | 92 | 0.46 | 0.80 | 25 | FAD, ACT |
| 4 | 50 | 0.28 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1014 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4U9U · Crystal structure of NqrF FAD-binding domain from Vibrio cholerae · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X4Q8 · AlphaFold monomer V2.0 prediction for na(+)-translocating NADH- quinone reductase subunit… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9X4Q8
- Elsewhere: RCSB PDB 4U9U · PDBe 4U9U · UniProt Q9X4Q8
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