Research workbench
Crystal structure of a nitroreductase family protein from agrobacterium tumefaciens str. C58
Analyse Crystal structure of a nitroreductase family protein from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K6H
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitroreductase family protein
- UniProt
- A9CIP6
- Ligands
- FMN, SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitroreductase family protein | protein | 191 | 40% helix, 18% strand | A9CIP6 |
| B | Nitroreductase family protein | protein | 191 | 43% helix, 18% strand | A9CIP6 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.57 | 0.81 | 22 | SO4, FMN |
| 2 | 166 | 0.55 | 0.81 | 22 | SO4, FMN |
| 3 | 115 | 0.38 | 0.74 | 17 | empty |
| 4 | 101 | 0.35 | 0.74 | 23 | empty |
| 5 | 62 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3379 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 3K6H · Crystal structure of a nitroreductase family protein from Agrobacterium tumefaciens str.… · 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 A9CIP6
- Elsewhere: RCSB PDB 3K6H · PDBe 3K6H · UniProt A9CIP6
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