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Crystal structure of bau-bound human uridine phosphorylase 1

Analyse Crystal structure of bau-bound human uridine phosphorylase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EUF
Type: protein
Length: 1,174 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uridine phosphorylase 1
EC: 2.4.2.3
UniProt: Q16831
Ligands: BAU, PO4
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Uridine phosphorylase 1 (EC 2.4.2.3)	protein	293	34% helix, 26% strand	Q16831
C, D	Uridine phosphorylase 1 (EC 2.4.2.3)	protein	294	37% helix, 26% strand	Q16831

Ligands and binding sites

BAU · 1-((2-hydroxyethoxy)methyl)-5-benzylpyrimidine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	446	0.81	0.89	60	BAU, PO4
2	1109	0.80	0.82	95	BAU, PO4
3	447	0.80	0.88	46	empty
4	434	0.78	0.87	42	empty
5	468	0.76	0.85	53	BAU, PO4

Interfaces

5 interfaces between chains.

C–D · 2952 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2930 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 342 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 202 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 186 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3EUF · Crystal structure of BAU-bound human uridine phosphorylase 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q16831 · AlphaFold monomer V2.0 prediction for uridine phosphorylase 1 (Q16831) · 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 Q16831
Elsewhere: RCSB PDB 3EUF · PDBe 3EUF · UniProt Q16831

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