Research workbench
Crystal structure of a nitroreductase family protein (CD3355) from clostridium difficile 630 at 1.58 a resolution
Analyse Crystal structure of a nitroreductase family protein (CD3355) from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KOQ
- Type
- protein
- Length
- 689 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitroreductase family protein
- UniProt
- Q180K0
- Ligands
- FMN, CL
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitroreductase family protein | protein | 173 | 38% helix, 21% strand | Q180K0 |
| B, C, D | Nitroreductase family protein | protein | 172 | 38% helix, 22% strand | Q180K0 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.69 | 0.82 | 40 | CL, FMN |
| 2 | 205 | 0.59 | 0.80 | 27 | FMN, GOL |
| 3 | 208 | 0.59 | 0.80 | 27 | GOL, FMN |
| 4 | 345 | 0.57 | 0.76 | 53 | empty |
| 5 | 184 | 0.55 | 0.79 | 28 | FMN, CL |
Interfaces
4 interfaces between chains.
- C–D · 3378 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 3362 Ų buried · 57 hydrogen bonds · protein-protein
- B–D · 317 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 215 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3KOQ · Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile… · 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 Q180K0
- Elsewhere: RCSB PDB 3KOQ · PDBe 3KOQ · UniProt Q180K0
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