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Urate oxidase from aspergillus flavus complexed with 5,6-diaminouracil

Analyse Urate oxidase from aspergillus flavus complexed with 5,6-diaminouracil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WS2
Type: protein
Length: 1,182 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: URN
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	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
D	Uricase (EC 1.7.3.3)	protein	294	28% helix, 41% strand	Q00511

Ligands and binding sites

URN · 5,6-diaminopyrimidine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, B, C, D

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1063	0.80	0.81	112	URN
2	1042	0.79	0.80	107	URN
3	202	0.58	0.80	21	empty
4	199	0.55	0.79	22	empty
5	204	0.55	0.79	22	empty

Interfaces

6 interfaces between chains.

C–D · 3056 Å² buried · 64 hydrogen bonds · protein-protein
A–B · 3007 Å² buried · 71 hydrogen bonds · protein-protein
A–C · 2698 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 2680 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 416 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (acetylation).

Compared structures

1WS2 · urate oxidase from aspergillus flavus complexed with 5,6-diaminouracil · the same entry in another collection · chain A against A, TM-score 1.00
Q00511 · AlphaFold monomer V2.0 prediction for uricase (Q00511) · a predicted model of the same protein · chain D 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 1WS2 · PDBe 1WS2 · UniProt Q00511

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