MolNFT v1 · #126652 · protein

Crystal structure of urate oxidase from zebrafish

5M98 · Uricase: “Crystal structure of urate oxidase from zebrafish”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #126652 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5M98
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
UniProt: Q6DG85
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 43% 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	24% helix, 43% strand	Q6DG85

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1163	0.80	0.81	106	empty
2	973	0.77	0.79	110	empty
3	690	0.72	0.78	77	empty
4	731	0.72	0.78	76	empty
5	638	0.70	0.77	65	empty

Interfaces

16 interfaces between chains.

A–B · 3225 Å² buried · 60 hydrogen bonds · protein-protein
G–H · 3216 Å² buried · 63 hydrogen bonds · protein-protein
E–F · 3184 Å² buried · 62 hydrogen bonds · protein-protein
C–D · 3166 Å² buried · 57 hydrogen bonds · protein-protein
E–G · 2953 Å² buried · 44 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5M98 · Crystal structure of urate oxidase from zebrafish · the same entry in another collection · chain H against H, TM-score 1.00
Q6DG85 · AlphaFold monomer V2.0 prediction for uricase (Q6DG85) · 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 Q6DG85
Elsewhere: RCSB PDB 5M98 · PDBe 5M98 · UniProt Q6DG85

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