Research workbench
Crystal structure of highly active mutant of bacillus sp. tb-90 urate oxidase
Analyse Crystal structure of highly active mutant of bacillus sp. tb-90 urate oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XFP
- Type
- protein
- Length
- 1,176 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, CL, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Urate oxidase (EC 1.7.3.3) | protein | 294 | 25% helix, 40% strand | Q45697 |
Ligands and binding sites
- AZA · 8-azaxanthine · ligand · 4 copies · chains A, B, C, D
- 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 | 879 | 0.76 | 0.80 | 78 | empty |
| 2 | 869 | 0.76 | 0.80 | 83 | empty |
| 3 | 475 | 0.69 | 0.80 | 65 | AZA, CL |
| 4 | 329 | 0.69 | 0.83 | 41 | AZA, CL |
| 5 | 450 | 0.68 | 0.80 | 59 | AZA, CL |
Interfaces
6 interfaces between chains.
- C–D · 2658 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2650 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2611 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 2568 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 269 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 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 4XFP · PDBe 4XFP · UniProt Q45697
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