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Crystal structure of the cofactor-devoid 1-H-3-hydroxy-4- oxoquinaldine 2,4-dioxygenase (hod) from arthrobacter nitroguajacolicus RU61A in complex with chloride
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
- 2WM2
- Type
- protein
- Length
- 1,103 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
- EC
- 1.13.11.48
- UniProt
- A4V8M9
- Ligands
- SRT, NA, K, CL
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% 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 | 49% helix, 16% strand | A4V8M9 |
| B | 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (EC 1.13.11.48) | protein | 275 | 48% helix, 16% strand | A4V8M9 |
| C, D | 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (EC 1.13.11.48) | protein | 277 | 49% helix, 15% strand | A4V8M9 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 7 copies · chains A, C, B, D
- NA · Sodium ion · metal · 12 copies · chains A, C, B, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.79 | 0.83 | 84 | GOL, CL, SRT, K |
| 2 | 611 | 0.78 | 0.84 | 71 | NA, CL, K |
| 3 | 189 | 0.66 | 0.85 | 34 | CL |
| 4 | 194 | 0.65 | 0.84 | 33 | GOL, CL |
| 5 | 165 | 0.54 | 0.80 | 23 | GOL, SRT |
Interfaces
2 interfaces between chains.
- A–C · 591 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 577 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2WM2 · 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 2WM2 · PDBe 2WM2 · UniProt A4V8M9
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