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Crystal structure of the cofactor-devoid 1-H-3-hydroxy-4- oxoquinaldine 2,4-dioxygenase (hod) from arthrobacter nitroguajacolicus RU61A
Analyse Crystal structure of the cofactor-devoid 1-H-3-hydroxy-4- oxoquinaldine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WJ3
- Type
- protein
- Length
- 1,093 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.09
- Source
- ARTHROBACTER NITROGUAJACOLICUS
- Molecule
- 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
- EC
- 1.13.11.48
- UniProt
- A4V8M9
- Ligands
- SRT
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.09 · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (EC 1.13.11.48) | protein | 274 | 50% helix, 16% strand | A4V8M9 |
| B | 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (EC 1.13.11.48) | protein | 273 | 49% helix, 16% strand | A4V8M9 |
| C, D | 1-H-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 · 8 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.79 | 0.82 | 86 | SRT |
| 2 | 842 | 0.79 | 0.82 | 86 | GOL, SRT |
| 3 | 193 | 0.66 | 0.85 | 31 | empty |
| 4 | 196 | 0.66 | 0.85 | 33 | empty |
| 5 | 52 | 0.27 | 0.74 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–C · 565 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 542 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2WJ3 · 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 2WJ3 · PDBe 2WJ3 · UniProt A4V8M9
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