Research workbench
Crystal structure of highly active btuo mutant P287G improved by humidity control at 83% rh
Analyse Crystal structure of highly active btuo mutant P287G 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
- 5Y52
- Type
- protein
- Length
- 1,182 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
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Uric acid degradation bifunctional protein (EC 4.1.1.97, 1.7.3.3) | protein | 295 | 25% helix, 40% strand | Q45697 |
| B, C | Uric acid degradation bifunctional protein (EC 4.1.1.97, 1.7.3.3) | protein | 296 | 25% 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 A, C, B, D
- EDO · 1,2-ethanediol · additive · 11 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 | 856 | 0.77 | 0.80 | 87 | EDO |
| 2 | 761 | 0.77 | 0.81 | 90 | AZA, OXY |
| 3 | 883 | 0.77 | 0.80 | 90 | EDO |
| 4 | 466 | 0.68 | 0.79 | 67 | AZA, OXY |
| 5 | 303 | 0.67 | 0.82 | 44 | AZA, OXY |
Interfaces
6 interfaces between chains.
- B–C · 2745 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 2651 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 2646 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2643 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5Y52 · Crystal Structure of Highly Active BTUO Mutant P287G Improved by Humidity Control at 83%… · 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 B 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 5Y52 · PDBe 5Y52 · UniProt Q45697
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