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Structure of uracil phosphoribosyl transferase

Analyse Structure of uracil phosphoribosyl transferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EHJ
Type: protein
Length: 832 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uracil phosphoribosyltransferase
EC: 2.4.2.9
UniProt: P0A8F0
Ligands: SO4
Pockets: 14 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Uracil phosphoribosyltransferase (EC 2.4.2.9)	protein	208	35% helix, 32% strand	P0A8F0

Ligands and binding sites

SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.89	0.90	95	empty
2	293	0.75	0.88	31	SO4
3	402	0.75	0.85	36	SO4
4	298	0.74	0.87	33	SO4
5	327	0.72	0.85	32	SO4

Interfaces

6 interfaces between chains.

A–D · 1890 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1820 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1095 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1072 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 116 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2EHJ · Structure of Uracil phosphoribosyl transferase · the same entry in another collection · chain A against A, TM-score 1.00
P0A8F0 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (P0A8F0) · 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 P0A8F0
Elsewhere: RCSB PDB 2EHJ · PDBe 2EHJ · UniProt P0A8F0

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