Research workbench
Structure of E. COLI uridine phosphorylase complexed with uracil and ribose 1-phosphate
Analyse Structure of E. COLI uridine phosphorylase complexed with uracil and ribose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TGY
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P12758
- Ligands
- R1P, URA, K
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 34% helix, 28% strand | P12758 |
Ligands and binding sites
- R1P · 1-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- URA · Uracil · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.65 | 0.80 | 39 | R1P, URA |
| 2 | 305 | 0.64 | 0.81 | 49 | R1P, URA |
| 3 | 106 | 0.38 | 0.75 | 25 | empty |
| 4 | 75 | 0.29 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1999 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1TGY · Structure of E. coli Uridine Phosphorylase complexed with uracil and ribose 1-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P12758 · AlphaFold monomer V2.0 prediction for uridine phosphorylase (P12758) · 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 P12758
- Elsewhere: RCSB PDB 1TGY · PDBe 1TGY · UniProt P12758
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