Research workbench
Hyperthermostable mutant of bacillus sp. tb-90 urate oxidase - R298C
Analyse Hyperthermostable mutant of bacillus sp. tb-90 urate oxidase - R298C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AYJ
- Type
- protein
- Length
- 1,197 residues
- Chains
- 4
- 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
- MUA, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uric acid degradation bifunctional protein (EC 1.7.3.3) | protein | 296 | 25% helix, 40% strand | Q45697 |
| B | Uric acid degradation bifunctional protein (EC 1.7.3.3) | protein | 303 | 25% helix, 41% strand | Q45697 |
| C | Uric acid degradation bifunctional protein (EC 1.7.3.3) | protein | 304 | 25% helix, 40% strand | Q45697 |
| D | Uric acid degradation bifunctional protein (EC 1.7.3.3) | protein | 294 | 25% helix, 38% strand | Q45697 |
Ligands and binding sites
- MUA · 9-methyl uric acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · 6 copies · chains A, B, C, 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 | 1056 | 0.75 | 0.78 | 110 | MUA |
| 2 | 703 | 0.74 | 0.80 | 69 | SO4 |
| 3 | 686 | 0.74 | 0.80 | 74 | SO4 |
| 4 | 500 | 0.68 | 0.79 | 62 | MUA |
| 5 | 312 | 0.66 | 0.81 | 42 | MUA |
Interfaces
6 interfaces between chains.
- B–C · 2721 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2664 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2637 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 2555 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 169 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5AYJ · Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C · the same entry in another collection · chain D against D, 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 D 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 5AYJ · PDBe 5AYJ · UniProt Q45697
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