Research workbench

Uprt-uracil complex

Analyse Uprt-uracil complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BD4
Type: protein
Length: 896 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uracil phosphoribosyltransferase
EC: 2.4.2.9
UniProt: Q26998
Ligands: URA, PO4
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, B, A	Uracil phosphoribosyltransferase (EC 2.4.2.9)	protein	224	39% helix, 26% strand	Q26998

Ligands and binding sites

URA · Uracil · ligand · 4 copies · chains D, C, B, A
PO4 · Phosphate ion · ion · 8 copies · chains D, B, C, A

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

Pockets

13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	918	0.82	0.84	88	empty
2	227	0.73	0.88	26	empty
3	467	0.72	0.82	35	PO4, URA
4	436	0.72	0.82	32	PO4, URA
5	403	0.69	0.81	34	PO4, URA

Interfaces

4 interfaces between chains.

D–A · 2124 Å² buried · 30 hydrogen bonds · protein-protein
C–B · 2100 Å² buried · 40 hydrogen bonds · protein-protein
C–A · 1158 Å² buried · 16 hydrogen bonds · protein-protein
D–B · 1065 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1BD4 · Uprt-uracil complex · the same entry in another collection · chain D against D, TM-score 1.00
Q26998 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (Q26998) · a predicted model of the same protein · chain D 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 Q26998
Elsewhere: RCSB PDB 1BD4 · PDBe 1BD4 · UniProt Q26998

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