Research workbench
Crystal structure of kynurenine formamidase from bacillus anthracis complexed with 2-aminoacetophenone.
Analyse Crystal structure of kynurenine formamidase from bacillus anthracis complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CZ1
- Type
- protein
- Length
- 825 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
- VNJ, ZN, MG
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kynurenine formamidase (EC 3.5.1.9) | protein | 207 | 16% helix, 28% strand | Q81PP9 |
| B, C, D | Kynurenine formamidase (EC 3.5.1.9) | protein | 206 | 17% helix, 28% strand | Q81PP9 |
Ligands and binding sites
- VNJ · 2-aminoacetophenone · ligand · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.67 | 0.78 | 65 | empty |
| 2 | 379 | 0.65 | 0.79 | 39 | empty |
| 3 | 124 | 0.61 | 0.86 | 24 | empty |
| 4 | 158 | 0.59 | 0.83 | 29 | empty |
| 5 | 139 | 0.58 | 0.84 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2485 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2485 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CZ1 · Crystal structure of kynurenine formamidase from Bacillus anthracis complexed with… · 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 B 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 4CZ1 · PDBe 4CZ1 · UniProt Q81PP9
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