MolNFT v1 · #159093 · protein

The crystal structure of hyper-thermostable aguricase mutant K12C/E286C

6OE8: “The crystal structure of hyper-thermostable aguricase mutant K12C/E286C”. X-ray diffraction, 14 pockets (best druggability 0.77). MolNFT v1 #159093 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OE8
Type: protein
Length: 1,168 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uricase
EC: 1.7.3.3
UniProt: D0VWQ1
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Uricase (EC 1.7.3.3)	protein	292	26% helix, 41% strand	D0VWQ1

Ligands and binding sites

PGE · Triethylene glycol · additive · 8 copies · chains A, B, D, C
MLI · Malonate ion · additive · 8 copies · chains A, D, B, C
PG4 · Tetraethylene glycol · additive · 5 copies · chains A, C, B, D

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	918	0.77	0.79	84	PGE, MLI
2	901	0.76	0.79	84	PGE, MLI
3	825	0.70	0.76	100	PG4, PGE, MLI
4	720	0.68	0.76	80	PG4, PGE, MLI
5	150	0.43	0.76	30	empty

Interfaces

6 interfaces between chains.

B–C · 3840 Å² buried · 56 hydrogen bonds · protein-protein
A–D · 3767 Å² buried · 57 hydrogen bonds · protein-protein
C–D · 2528 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 2506 Å² buried · 47 hydrogen bonds · protein-protein
B–D · 487 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6OE8 · The crystal structure of hyper-thermostable AgUricase mutant K12C/E286C · the same entry in another collection · chain A against A, TM-score 1.00
D0VWQ1 · AlphaFold monomer V2.0 prediction for uricase (D0VWQ1) · 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 D0VWQ1
Elsewhere: RCSB PDB 6OE8 · PDBe 6OE8 · UniProt D0VWQ1

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