MolNFT v1 · #55924 · protein

Crystal structure of uricase from arthrobacter globiformis in complex with 8-azaxanthin (inhibitor)

2YZD: “Crystal structure of uricase from arthrobacter globiformis in complex with 8-azaxanthin (inhibitor)”. X-ray diffraction, 1 ligand (AZA), 20 pockets (best druggability 0.80). MolNFT v1 #55924 on GenesisL1: 3D structure, binding sites…

PDB: 2YZD
Type: protein
Length: 2,296 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uricase
EC: 1.7.3.3
Ligands: AZA
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Uricase (EC 1.7.3.3)	protein	287	25% helix, 42% strand	—

Ligands and binding sites

AZA · 8-azaxanthine · ligand · 8 copies · chains A, D, B, C, E, H, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1021	0.80	0.81	103	AZA
2	875	0.77	0.80	87	AZA
3	865	0.76	0.79	85	AZA
4	463	0.72	0.82	48	AZA
5	1066	0.71	0.75	90	empty

Interfaces

15 interfaces between chains.

B–C · 3297 Å² buried · 56 hydrogen bonds · protein-protein
F–G · 3282 Å² buried · 54 hydrogen bonds · protein-protein
A–D · 3277 Å² buried · 56 hydrogen bonds · protein-protein
E–H · 3252 Å² buried · 54 hydrogen bonds · protein-protein
G–H · 2466 Å² buried · 46 hydrogen bonds · protein-protein

Compared structures

2YZD · Crystal structure of uricase from Arthrobacter globiformis in complex with 8-azaxanthin… · 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
Elsewhere: RCSB PDB 2YZD · PDBe 2YZD

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