MolNFT v1 · #27915 · protein
Urate oxidase from aspergillus flavus complexed with guanine
1XY3 · Uricase: “Urate oxidase from aspergillus flavus complexed with guanine”. X-ray diffraction, 1 ligand (GUN), 20 pockets (best druggability 0.84). MolNFT v1 #27915 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XY3
- Type
- protein
- Length
- 2,363 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uricase
- EC
- 1.7.3.3
- UniProt
- Q00511
- Ligands
- GUN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | Uricase (EC 1.7.3.3) | protein | 295 | 27% helix, 42% strand | Q00511 |
| C | Uricase (EC 1.7.3.3) | protein | 298 | 27% helix, 42% strand | Q00511 |
Ligands and binding sites
- GUN · Guanine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.84 | 0.85 | 142 | GUN |
| 2 | 1116 | 0.79 | 0.81 | 112 | GUN |
| 3 | 1081 | 0.79 | 0.80 | 113 | GUN |
| 4 | 1099 | 0.79 | 0.80 | 111 | GUN |
| 5 | 194 | 0.57 | 0.80 | 19 | empty |
Interfaces
14 interfaces between chains.
- E–F · 2995 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 2984 Ų buried · 66 hydrogen bonds · protein-protein
- G–H · 2984 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 2974 Ų buried · 60 hydrogen bonds · protein-protein
- F–H · 2691 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (acetylation).
Compared structures
- 1XY3 · Urate oxidase from aspergillus flavus complexed with guanine · the same entry in another collection · 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 Q00511
- Elsewhere: RCSB PDB 1XY3 · PDBe 1XY3 · UniProt Q00511
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