Research workbench
Thermostable urate oxidase from bacillus sp. tb-90
Analyse Thermostable urate oxidase from bacillus sp. tb-90 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WLV
- Type
- protein
- Length
- 1,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urate oxidase
- EC
- 1.7.3.3
- UniProt
- Q45697
- Ligands
- AZA, K, CL, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Urate oxidase (EC 1.7.3.3) | protein | 303 | 24% helix, 40% strand | Q45697 |
Ligands and binding sites
- AZA · 8-azaxanthine · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 2 copies · chains B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.76 | 0.80 | 87 | empty |
| 2 | 873 | 0.76 | 0.79 | 75 | empty |
| 3 | 340 | 0.69 | 0.83 | 43 | AZA, CL |
| 4 | 502 | 0.69 | 0.79 | 67 | AZA, CL |
| 5 | 454 | 0.69 | 0.80 | 59 | AZA, CL |
Interfaces
6 interfaces between chains.
- B–C · 2805 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 2794 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2687 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2683 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3WLV · Thermostable urate oxidase from Bacillus sp. TB-90 · the same entry in another collection · chain A against A, TM-score 1.00
- Q45697 · AlphaFold monomer V2.0 prediction for uric acid degradation bifunctional protein (Q45697) · a predicted model of the same protein · 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 Q45697
- Elsewhere: RCSB PDB 3WLV · PDBe 3WLV · UniProt Q45697
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