MolNFT v1 · #190592 · protein
Cryo-EM structure of na+-pumping NADH-ubiquinone oxidoreductase from vibrio cholerae, with korormicin
7XK7: “Cryo-EM structure of na+-pumping NADH-ubiquinone oxidoreductase from vibrio cholerae, with korormicin”. Electron microscopy, 7 ligands (PEE, FMN, FES). MolNFT v1 #190592 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XK7
- Type
- protein
- Length
- 1,921 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- A5F5X1, A5F5X0, A5F5Y7, A5F5Y6, A5F5Y5, A5F5Y4
- Ligands
- PEE, FMN, FES, RBF, IQT, FAD, CA
Structure
electron microscopy · 6 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 446 | — | A5F5X1 |
| B | — | protein | 412 | — | A5F5X0 |
| C | — | protein | 251 | — | A5F5Y7 |
| D | — | protein | 206 | — | A5F5Y6 |
| E | — | protein | 198 | — | A5F5Y5 |
| F | — | protein | 408 | — | A5F5Y4 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains B, C, D, F
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, C
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains D, E, F
- RBF · Riboflavin · ligand · chains B
- IQT · Korormicin · ligand · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · chains F
- CA · Calcium ion · metal · chains C
- 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.
Compared structures
- 7XK7 · Cryo-EM structure of Na+-pumping NADH-ubiqui oxidoreductase from Vibrio cholerae, with… · 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 0.94
- 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 0.93
- 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 0.91
- 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 0.87
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 7XK7 · PDBe 7XK7 · UniProt A5F5X1 · UniProt A5F5X0 · UniProt A5F5Y7 · UniProt A5F5Y6 · UniProt A5F5Y5 · UniProt A5F5Y4
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