MolNFT v1 · #27897 · protein
Urate oxidase from aspergillus flavus complexed with 5-amino 6-nitro uracil
1XXJ · Uricase: “Urate oxidase from aspergillus flavus complexed with 5-amino 6-nitro uracil”. X-ray diffraction, 2 ligands (UNC, BNZ), 13 pockets (best druggability 0.78). MolNFT v1 #27897 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1XXJ
- Type
- protein
- Length
- 1,179 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uricase
- EC
- 1.7.3.3
- UniProt
- Q00511
- Ligands
- UNC, BNZ
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Uricase (EC 1.7.3.3) | protein | 295 | 27% helix, 42% strand | Q00511 |
| B | Uricase (EC 1.7.3.3) | protein | 294 | 27% helix, 42% strand | Q00511 |
Ligands and binding sites
- UNC · 5-amino-6-nitropyrimidine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, B, C, D
- BNZ · Benzene · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.78 | 0.80 | 105 | UNC |
| 2 | 1017 | 0.78 | 0.80 | 103 | UNC |
| 3 | 201 | 0.56 | 0.79 | 22 | empty |
| 4 | 192 | 0.56 | 0.79 | 21 | empty |
| 5 | 200 | 0.54 | 0.78 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2979 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 2953 Ų buried · 64 hydrogen bonds · protein-protein
- B–D · 2697 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2672 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 416 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 1XXJ · Urate oxidase from aspergillus flavus complexed with 5-amino 6-nitro uracil · 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 1XXJ · PDBe 1XXJ · UniProt Q00511
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