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Uncomplexed urate oxidase from aspergillus flavus

Analyse Uncomplexed urate oxidase from aspergillus flavus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1R56
Type: protein
Length: 2,364 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uricase
EC: 1.7.3.3
UniProt: Q00511
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 41% 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	299	27% helix, 41% strand	Q00511

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1116	0.81	0.82	134	empty
2	1111	0.79	0.81	115	empty
3	1077	0.79	0.80	110	PEG
4	1079	0.79	0.80	110	empty
5	202	0.57	0.80	20	empty

Interfaces

14 interfaces between chains.

A–B · 2994 Å² buried · 64 hydrogen bonds · protein-protein
E–F · 2988 Å² buried · 67 hydrogen bonds · protein-protein
C–D · 2987 Å² buried · 65 hydrogen bonds · protein-protein
G–H · 2962 Å² buried · 60 hydrogen bonds · protein-protein
F–H · 2686 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (acetylation).

Compared structures

1R56 · Uncomplexed urate oxidase from aspergillus flavus · the same entry in another collection · chain H against H, TM-score 1.00
Q00511 · AlphaFold monomer V2.0 prediction for uricase (Q00511) · a predicted model of the same protein · chain A 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 Q00511
Elsewhere: RCSB PDB 1R56 · PDBe 1R56 · UniProt Q00511

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