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Crystal structure of cofactor-free urate oxidase in complex with its 5-peroxoisourate intermediate (X-ray dose, 2.2 kgy)
Analyse Crystal structure of cofactor-free urate oxidase in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D13
- Type
- protein
- Length
- 295 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uricase
- EC
- 1.7.3.3
- UniProt
- Q00511
- Ligands
- IUP
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uricase (EC 1.7.3.3) | protein | 295 | 28% helix, 39% strand | Q00511 |
Ligands and binding sites
- IUP · 5-(hydro)peroxoisourate · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.55 | 0.78 | 21 | empty |
| 2 | 200 | 0.49 | 0.76 | 23 | IUP |
Compared structures
- 4D13 · Crystal structure of cofactor-free urate oxidase in complex with its 5-peroxoisourate… · 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 4D13 · PDBe 4D13 · UniProt Q00511
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