Research workbench
The structure of E. COLI nitroreductase bound with the antibiotic nitrofurazone
Analyse The structure of E. COLI nitroreductase bound with the antibiotic nitrofurazone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YKI
- Type
- protein
- Length
- 866 residues
- Chains
- 4
- 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, NFZ
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.5.1.34) | protein | 216 | 55% helix, 15% strand | P38489 |
| B, D | Oxygen-insensitive NAD(P)H nitroreductase (EC 1.5.1.34) | protein | 217 | 56% helix, 15% strand | P38489 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- NFZ · Nitrofurazone · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains B, C, D
- CIT · Citric acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.77 | 0.81 | 89 | FMN, NFZ |
| 2 | 504 | 0.74 | 0.82 | 49 | FMN, NFZ, CIT, DMS |
| 3 | 491 | 0.73 | 0.82 | 46 | FMN, NFZ |
| 4 | 515 | 0.73 | 0.82 | 43 | FMN, NFZ |
| 5 | 195 | 0.54 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3666 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3641 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 501 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1YKI · The structure of E. coli nitroreductase bound with the antibiotic nitrofurazone · 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 B 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 1YKI · PDBe 1YKI · UniProt P38489
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