Research workbench

Human uridine phosphorylase 1 (HUPP1) with 5-fluorouracil

Analyse Human uridine phosphorylase 1 (HUPP1) with 5-fluorouracil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NBQ
Type: protein
Length: 1,172 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: URF
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Uridine phosphorylase 1 (EC 2.4.2.3)	protein	293	35% helix, 26% strand	Q16831

Ligands and binding sites

URF · 5-fluorouracil · ligand · 4 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.81	0.84	108	URF
2	396	0.79	0.88	44	empty
3	417	0.79	0.88	44	empty
4	558	0.75	0.82	72	URF
5	350	0.73	0.85	48	URF

Interfaces

3 interfaces between chains.

A–B · 2992 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2942 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 500 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3NBQ · Human uridine phosphorylase 1 (hUPP1) with 5-fluorouracil · 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 3NBQ · PDBe 3NBQ · UniProt Q16831

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