MolNFT v1 · #53051 · protein
Crystal structure of the cofactor-devoid 1-H-3-hydroxy-4- oxoquinaldine 2,4-dioxygenase (hod) from arthrobacter nitroguajacolicus RU61A anaerobically complexed with its natural substrate 1-H-3-hydroxy-4-oxoquinaldine
2WJ4 · 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase: “Crystal structure of the cofactor-devoid 1-H-3-hydroxy-4- oxoquinaldine 2,4-dioxygenase (hod) from…”. X-ray diffraction, 3 ligands (SRT, HQD, K), 4 pockets (best druggability 0.79).…
- PDB
- 2WJ4
- Type
- protein
- Length
- 1,093 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
- EC
- 1.13.11.48
- UniProt
- A4V8M9
- Ligands
- SRT, HQD, K
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (EC 1.13.11.48) | protein | 274 | 50% helix, 16% strand | A4V8M9 |
| B | 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (EC 1.13.11.48) | protein | 273 | 49% helix, 16% strand | A4V8M9 |
| C, D | 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (EC 1.13.11.48) | protein | 273 | 49% helix, 15% strand | A4V8M9 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 7 copies · chains A, C, B, D
- HQD · 3-hydroxy-2-methylquinolin-4(1H)-one · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.79 | 0.82 | 84 | GOL, HQD, SRT, K |
| 2 | 813 | 0.78 | 0.81 | 82 | GOL, HQD, SRT, K |
| 3 | 187 | 0.67 | 0.86 | 34 | HQD |
| 4 | 199 | 0.66 | 0.84 | 37 | HQD |
Interfaces
2 interfaces between chains.
- A–C · 572 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 540 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2WJ4 · Crystal structure of the cofactor-devoid 1-H-3-hydroxy-4- oxoquinaldine 2,4-dioxygenase… · 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 A4V8M9
- Elsewhere: RCSB PDB 2WJ4 · PDBe 2WJ4 · UniProt A4V8M9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.