Research workbench
Crystal structure of kynurenine formamidase from burkholderia cenocepacia
Analyse Crystal structure of kynurenine formamidase from burkholderia cenocepacia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4COG
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kynurenine formamidase
- EC
- 3.5.1.9
- UniProt
- B4E9I9
- Ligands
- MG, ZN, CD
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Kynurenine formamidase (EC 3.5.1.9) | protein | 207 | 16% helix, 28% strand | B4E9I9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CD · Cadmium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.81 | 0.84 | 99 | CD, GOL, EDO |
| 2 | 591 | 0.77 | 0.83 | 75 | GOL |
| 3 | 275 | 0.74 | 0.87 | 48 | CD, GOL |
| 4 | 109 | 0.57 | 0.85 | 23 | empty |
| 5 | 77 | 0.37 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2382 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2339 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 276 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 109 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4COG · Crystal structure of kynurenine formamidase from Burkholderia cenocepacia · the same entry in another collection · chain A against A, TM-score 1.00
- B4E9I9 · AlphaFold monomer V2.0 prediction for kynurenine formamidase (B4E9I9) · a predicted model of the same protein · 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 B4E9I9
- Elsewhere: RCSB PDB 4COG · PDBe 4COG · UniProt B4E9I9
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