Research workbench
E. coli NfsB-T41Q/N71S/F124T mutant bound to acetate
Analyse E. coli NfsB-T41Q/N71S/F124T mutant bound to acetate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8C5F
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Escherichia coli
- Molecule
- Oxygen-insensitive NAD(P)H nitroreductase
- EC
- 1.-.-.-, 1.5.1.34
- UniProt
- P38489
- Ligands
- FMN
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.-.-.-, 1.5.1.34) | protein | 216 | 55% helix, 15% strand | P38489 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- ACT · Acetate ion · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.75 | 0.80 | 67 | FMN, ACT, EDO |
| 2 | 747 | 0.73 | 0.79 | 68 | ACT, EDO, FMN |
Interfaces
1 interface between chains.
- A–B · 3443 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- P38489 · AlphaFold monomer V2.0 prediction for oxygen-insensitive NAD(P)H nitroreductase (P38489) · 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 P38489
- Elsewhere: RCSB PDB 8C5F · PDBe 8C5F · UniProt P38489
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