MolNFT v1 · #140698 · protein
Crystal structure of bacillus sp. tb-90 urate oxidase without dehydration
5YJ2 · Uric acid degradation bifunctional protein: “Crystal structure of bacillus sp. tb-90 urate oxidase without dehydration”. X-ray diffraction, 3 ligands (AZA, OXY, SO4), 7 pockets (best druggability 0.77). MolNFT v1 #140698 on…
- PDB
- 5YJ2
- Type
- protein
- Length
- 1,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uric acid degradation bifunctional protein
- EC
- 4.1.1.97, 1.7.3.3
- UniProt
- Q45697
- Ligands
- AZA, OXY, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Uric acid degradation bifunctional protein (EC 4.1.1.97, 1.7.3.3) | protein | 303 | 24% helix, 41% strand | Q45697 |
Ligands and binding sites
- AZA · 8-azaxanthine · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, D, A, C
- MXE · 2-methoxyethanol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.77 | 0.81 | 105 | AZA, OXY |
| 2 | 862 | 0.77 | 0.80 | 87 | empty |
| 3 | 822 | 0.76 | 0.80 | 85 | empty |
| 4 | 472 | 0.69 | 0.80 | 66 | AZA, OXY |
| 5 | 321 | 0.68 | 0.82 | 41 | AZA, OXY |
Interfaces
6 interfaces between chains.
- A–D · 2796 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 2777 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2675 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2663 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5YJ2 · Crystal structure of Bacillus sp. TB-90 urate oxidase without dehydration · 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 5YJ2 · PDBe 5YJ2 · UniProt Q45697
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