MolNFT v1 · #111421 · protein
Crystal structure of E. COLI wrba in complex with benzoquinone
4YQE · NAD(P)H dehydrogenase (quinone): “Crystal structure of E. COLI wrba in complex with benzoquinone”. X-ray diffraction, 2 ligands (FMN, PLQ), 2 pockets (best druggability 0.71). MolNFT v1 #111421 on GenesisL1: 3D structure, binding…
- PDB
- 4YQE
- Type
- protein
- Length
- 380 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H dehydrogenase (quinone)
- EC
- 1.6.5.2
- UniProt
- P0A8G6
- Ligands
- FMN, PLQ
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 186 | 40% helix, 20% strand | P0A8G6 |
| B | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 194 | 40% helix, 17% strand | P0A8G6 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- PLQ · 1,4-benzoquinone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.71 | 0.77 | 76 | FMN, PLQ |
| 2 | 50 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 889 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4YQE · Crystal structure of E. coli WrbA in complex with benzoqui · the same entry in another collection · chain A against A, TM-score 1.00
- P0A8G6 · AlphaFold monomer V2.0 prediction for NAD(P)H dehydrogenase (quinone) (P0A8G6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A8G6
- Elsewhere: RCSB PDB 4YQE · PDBe 4YQE · UniProt P0A8G6
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