Research workbench
Crystal structure of a putative nitroreductase in complex with FMN (CD3205) from clostridium difficile 630 at 1.35 a resolution
Analyse Crystal structure of a putative nitroreductase in complex with FMN (CD3205)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GFA
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nitroreductase
- UniProt
- Q17ZU8
- Ligands
- FMN, CL
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nitroreductase | protein | 197 | 51% helix, 17% strand | Q17ZU8 |
| B | Putative nitroreductase | protein | 196 | 53% helix, 17% strand | Q17ZU8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 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 | 277 | 0.74 | 0.87 | 37 | CL, FMN, MRD |
| 2 | 268 | 0.73 | 0.87 | 36 | FMN, CL, MPD |
Interfaces
1 interface between chains.
- A–B · 3759 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 3GFA · Crystal structure of a putative nitroreductase in complex with fmn (cd3205) 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 Q17ZU8
- Elsewhere: RCSB PDB 3GFA · PDBe 3GFA · UniProt Q17ZU8
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