Research workbench
Crystal structure of the FMN-dependent nitroreductase nfnb from mycobacterium smegmatis in complex with NADPH
Analyse Crystal structure of the FMN-dependent nitroreductase nfnb from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WZW
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nfnb protein
- UniProt
- A0R6D0
- Ligands
- FMN, NDP, PO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nfnb protein | protein | 222 | 52% helix, 17% strand | A0R6D0 |
| B | Nfnb protein | protein | 223 | 51% helix, 16% strand | A0R6D0 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.75 | 0.82 | 73 | PO4, FMN |
| 2 | 587 | 0.75 | 0.82 | 59 | FMN, NDP, PO4 |
| 3 | 82 | 0.35 | 0.76 | 17 | empty |
| 4 | 82 | 0.32 | 0.74 | 21 | empty |
| 5 | 67 | 0.32 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3865 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2WZW · Crystal structure of the FMN-dependent nitroreductase NfnB from Mycobacterium smegmatis… · the same entry in another collection · chain A against A, TM-score 1.00
- A0R6D0 · AlphaFold monomer V2.0 prediction for nitroreductase nfnb (A0R6D0) · 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 A0R6D0
- Elsewhere: RCSB PDB 2WZW · PDBe 2WZW · UniProt A0R6D0
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