Research workbench
Crystal structure of highly active btuo mutant P287G without dehydration
Analyse Crystal structure of highly active btuo mutant P287G without dehydration in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YJA
- Type
- protein
- Length
- 1,195 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, K, OXY, SO4
- Pockets
- 7 · best druggability 0.78
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 4.1.1.97, 1.7.3.3) | protein | 298 | 25% helix, 40% strand | Q45697 |
| B | Uric acid degradation bifunctional protein (EC 4.1.1.97, 1.7.3.3) | protein | 302 | 25% helix, 39% strand | Q45697 |
| C | Uric acid degradation bifunctional protein (EC 4.1.1.97, 1.7.3.3) | protein | 299 | 25% helix, 40% strand | Q45697 |
| D | 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
- K · Potassium ion · metal · 2 copies · chains B, C
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D
- MXE · 2-methoxyethanol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.78 | 0.81 | 102 | AZA, OXY |
| 2 | 834 | 0.76 | 0.79 | 78 | MXE |
| 3 | 430 | 0.70 | 0.81 | 58 | AZA, OXY |
| 4 | 394 | 0.68 | 0.81 | 46 | SO4, AZA, OXY |
| 5 | 430 | 0.68 | 0.80 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2810 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 2760 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2579 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2546 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 445 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5YJA · Crystal structure of highly active BTUO mutant P287G without dehydration · 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 C against A, TM-score 0.99
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 5YJA · PDBe 5YJA · UniProt Q45697
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