Research workbench

Urate oxidase from aspergillus flavus complexed with 5-amino 6-nitro uracil

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

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.

Pocket	Volume (Å³)	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 Å² buried · 71 hydrogen bonds · protein-protein
A–B · 2953 Å² buried · 64 hydrogen bonds · protein-protein
B–D · 2697 Å² buried · 40 hydrogen bonds · protein-protein
A–C · 2672 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 416 Å² 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

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.