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Crystal structure of bacillus sp. tb-90 urate oxidase improved by humidity control at 89% rh
Analyse Crystal structure of bacillus sp. tb-90 urate oxidase improved by humidity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y2P
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uric acid degradation bifunctional protein
- EC
- 1.7.3.3
- UniProt
- Q45697
- Ligands
- AZA, K, OXY, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uric acid degradation bifunctional protein (EC 1.7.3.3) | protein | 303 | 24% helix, 40% strand | Q45697 |
| B | Uric acid degradation bifunctional protein (EC 1.7.3.3) | protein | 304 | 24% helix, 41% strand | Q45697 |
Ligands and binding sites
- AZA · 8-azaxanthine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 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 | 277 | 0.66 | 0.82 | 35 | AZA, OXY |
| 2 | 264 | 0.66 | 0.82 | 32 | AZA, OXY |
| 3 | 268 | 0.64 | 0.81 | 35 | EDO |
| 4 | 245 | 0.64 | 0.82 | 32 | EDO |
| 5 | 50 | 0.25 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2655 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5Y2P · Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 89%… · 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 5Y2P · PDBe 5Y2P · UniProt Q45697
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