MolNFT v1 · #88223 · protein
Crystal structure of kynurenine formamidase from bacillus anthracis
4CO9: “Crystal structure of kynurenine formamidase from bacillus anthracis”. X-ray diffraction, 3 ligands (GXT, ZN, MG), 7 pockets (best druggability 0.68). MolNFT v1 #88223 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CO9
- Type
- protein
- Length
- 826 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kynurenine formamidase
- EC
- 3.5.1.9
- UniProt
- Q81PP9
- Ligands
- GXT, ZN, MG
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kynurenine formamidase (EC 3.5.1.9) | protein | 207 | 16% helix, 28% strand | Q81PP9 |
| C, D | Kynurenine formamidase (EC 3.5.1.9) | protein | 206 | 17% helix, 28% strand | Q81PP9 |
Ligands and binding sites
- GXT · ethanedial · ligand · 3 copies · chains A, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, D, C
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.68 | 0.78 | 60 | empty |
| 2 | 277 | 0.61 | 0.80 | 23 | empty |
| 3 | 128 | 0.58 | 0.84 | 23 | ZN |
| 4 | 141 | 0.58 | 0.84 | 27 | empty |
| 5 | 125 | 0.57 | 0.84 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2509 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2495 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 480 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 82 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4CO9 · Crystal structure of kynurenine formamidase from Bacillus anthracis · the same entry in another collection · chain A against A, TM-score 1.00
- Q81PP9 · AlphaFold monomer V2.0 prediction for kynurenine formamidase (Q81PP9) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q81PP9
- Elsewhere: RCSB PDB 4CO9 · PDBe 4CO9 · UniProt Q81PP9
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