Research workbench
Crystal structure of the na+-translocating NADH: ubiquinone oxidoreductase from vibrio cholerae
Analyse Crystal structure of the na+-translocating NADH: ubiquinone oxidoreductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P6V
- Type
- protein
- Length
- 1,774 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Na(+)-translocating NADH-quinone reductase subunit a; Na(+)-translocating NADH-quinone…
- EC
- 1.6.5.-
- UniProt
- Q9KPS1, Q9KPS2, P0C6E0, Q9X4Q6, Q9X4Q7, Q9X4Q8
- Ligands
- FMN, RBF, FES, FAD, CA, FE
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Na(+)-translocating NADH-quinone reductase subunit a (EC 1.6.5.-) | protein | 400 | 27% helix, 26% strand | Q9KPS1 |
| B | Na(+)-translocating NADH-quinone reductase subunit B (EC 1.6.5.-) | protein | 348 | 57% helix, 0% strand | Q9KPS2 |
| C | Na(+)-translocating NADH-quinone reductase subunit C (EC 1.6.5.-) | protein | 251 | 39% helix, 25% strand | P0C6E0 |
| D | Na(+)-translocating NADH-quinone reductase subunit D (EC 1.6.5.-) | protein | 179 | 68% helix, 0% strand | Q9X4Q6 |
| E | Na(+)-translocating NADH-quinone reductase subunit E (EC 1.6.5.-) | protein | 189 | 73% helix, 1% strand | Q9X4Q7 |
| F | Na(+)-translocating NADH-quinone reductase subunit F (EC 1.6.5.-) | protein | 407 | 31% helix, 23% strand | Q9X4Q8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, C, D, E
- RBF · Riboflavin · ligand · chains B, E
- FES · Fe2/s2 (inorganic) cluster · ligand · chains F
- FAD · Flavin-adenine dinucleotide · ligand · chains F
- CA · Calcium ion · metal · chains C
- FE · Fe (III) ion · metal · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.87 | 0.88 | 81 | FMN |
| 2 | 1106 | 0.85 | 0.85 | 110 | FMN |
| 3 | 735 | 0.81 | 0.85 | 75 | empty |
| 4 | 690 | 0.79 | 0.83 | 102 | empty |
| 5 | 697 | 0.70 | 0.77 | 70 | FAD |
Interfaces
12 interfaces between chains.
- D–E · 1776 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1706 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1319 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 878 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 756 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 covalent (flavinylation, covalent ligand).
Compared structures
- Q9KPS1 · 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 0.99
- P0C6E0 · AlphaFold monomer V2.0 prediction for na(+)-translocating NADH- quinone reductase subunit… · a predicted model of the same protein · chain C against A, TM-score 0.95
- Q9KPS2 · AlphaFold monomer V2.0 prediction for na(+)-translocating NADH- quinone reductase subunit… · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q9X4Q7 · AlphaFold monomer V2.0 prediction for na(+)-translocating NADH- quinone reductase subunit… · a predicted model of the same protein · chain E against A, TM-score 0.94
- Q9X4Q6 · AlphaFold monomer V2.0 prediction for na(+)-translocating NADH- quinone reductase subunit… · a predicted model of the same protein · chain D against A, TM-score 0.94
- Q9X4Q8 · AlphaFold monomer V2.0 prediction for na(+)-translocating NADH- quinone reductase subunit… · a predicted model of the same protein · chain F against A, TM-score 0.89
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 Q9KPS1
- Every structure of UniProt Q9KPS2
- Every structure of UniProt P0C6E0
- Every structure of UniProt Q9X4Q6
- Every structure of UniProt Q9X4Q7
- Every structure of UniProt Q9X4Q8
- Elsewhere: RCSB PDB 4P6V · PDBe 4P6V · UniProt Q9KPS1 · UniProt Q9KPS2 · UniProt P0C6E0 · UniProt Q9X4Q6 · UniProt Q9X4Q7 · UniProt Q9X4Q8
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