MolNFT v1 · #28688 · protein
The structure of E. COLI nitroreductase with bound acetate, crystal form 2
1YLU · Oxygen-insensitive NAD(P)H nitroreductase: “The structure of E. COLI nitroreductase with bound acetate, crystal form 2”. X-ray diffraction, 1 ligand (FMN), 4 pockets (best druggability 0.74). MolNFT v1 #28688 on GenesisL1: 3D…
- PDB
- 1YLU
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxygen-insensitive NAD(P)H nitroreductase
- EC
- 1.5.1.34
- UniProt
- P38489
- Ligands
- FMN
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.5.1.34) | protein | 216 | 55% helix, 15% strand | P38489 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.74 | 0.83 | 48 | ACT, FMN |
| 2 | 496 | 0.73 | 0.82 | 46 | FMN, ACT |
| 3 | 191 | 0.50 | 0.77 | 25 | empty |
| 4 | 186 | 0.49 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3644 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 1YLU · The structure of E. coli nitroreductase with bound acetate, crystal form 2 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 1YLU · PDBe 1YLU · UniProt P38489
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