Research workbench
Cryo-EM structure of na+-pumping NADH-ubiquinone oxidoreductase from vibrio cholerae, state 2
Analyse Cryo-EM structure of na+-pumping NADH-ubiquinone oxidoreductase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XK4
- Type
- protein
- Length
- 1,894 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Na(+)-translocating NADH-quinone reductase subunit a; Na(+)-translocating NADH-quinone…
- EC
- 7.2.1.1
- UniProt
- A5F5X1, A5F5X0, A5F5Y7, A5F5Y6, A5F5Y5, A5F5Y4
- Ligands
- FMN, PEE, FES, RBF, FAD, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Na(+)-translocating NADH-quinone reductase subunit a (EC 7.2.1.1) | protein | 446 | 24% helix, 24% strand | A5F5X1 |
| B | Na(+)-translocating NADH-quinone reductase subunit B (EC 7.2.1.1) | protein | 387 | 63% helix, 2% strand | A5F5X0 |
| C | Na(+)-translocating NADH-quinone reductase subunit C (EC 7.2.1.1) | protein | 251 | 37% helix, 25% strand | A5F5Y7 |
| D | Na(+)-translocating NADH-quinone reductase subunit D (EC 7.2.1.1) | protein | 204 | 70% helix, 3% strand | A5F5Y6 |
| E | Na(+)-translocating NADH-quinone reductase subunit E (EC 7.2.1.1) | protein | 198 | 73% helix, 0% strand | A5F5Y5 |
| F | Na(+)-translocating NADH-quinone reductase subunit F (EC 7.2.1.1) | protein | 408 | 32% helix, 24% strand | A5F5Y4 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, C
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains D, E, F
- RBF · Riboflavin · ligand · chains B
- FAD · Flavin-adenine dinucleotide · ligand · chains F
- CA · Calcium ion · metal · chains E
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.84 | 0.87 | 109 | FMN |
| 2 | 149 | 0.81 | 0.97 | 28 | RBF |
| 3 | 772 | 0.79 | 0.83 | 79 | empty |
| 4 | 874 | 0.72 | 0.77 | 82 | FAD |
| 5 | 254 | 0.70 | 0.85 | 28 | empty |
Interfaces
13 interfaces between chains.
- A–B · 3158 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 1828 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 1350 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 824 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 746 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 7XK4 · Cryo-EM structure of Na+-pumping NADH-ubiqui oxidoreductase from Vibrio cholerae, state 2 · the same entry in another collection · chain F against F, TM-score 1.00
- A5F5X1 · 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
- A5F5X0 · 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 0.97
- A5F5Y6 · 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 0.95
- A5F5Y5 · 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 0.92
- A5F5Y4 · 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 0.92
- A5F5Y7 · 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 0.86
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 A5F5X1
- Every structure of UniProt A5F5X0
- Every structure of UniProt A5F5Y7
- Every structure of UniProt A5F5Y6
- Every structure of UniProt A5F5Y5
- Every structure of UniProt A5F5Y4
- Elsewhere: RCSB PDB 7XK4 · PDBe 7XK4 · UniProt A5F5X1 · UniProt A5F5X0 · UniProt A5F5Y7 · UniProt A5F5Y6 · UniProt A5F5Y5 · UniProt A5F5Y4
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