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Crystal structure of FMN and NADPH-dependent nitroreductase nfnb mutant Y88A derived from sphigopyxis sp. strain hmh
Analyse Crystal structure of FMN and NADPH-dependent nitroreductase nfnb mutant Y88A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DP1
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitroreductase family protein
- UniProt
- A0A2L0VUJ4
- Ligands
- FMN
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitroreductase family protein | protein | 217 | 50% helix, 18% strand | A0A2L0VUJ4 |
| B | Nitroreductase family protein | protein | 214 | 50% helix, 18% strand | A0A2L0VUJ4 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.74 | 0.82 | 44 | FMN |
| 2 | 502 | 0.73 | 0.82 | 48 | FMN |
| 3 | 104 | 0.39 | 0.76 | 21 | empty |
| 4 | 83 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3668 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 7DP1 · Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88A derived from… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A2L0VUJ4
- Elsewhere: RCSB PDB 7DP1 · PDBe 7DP1 · UniProt A0A2L0VUJ4
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