Research workbench
Structure of E. COLI uridine phosphorylase complexed with 5- fluorouridine and sulfate
Analyse Structure of E. COLI uridine phosphorylase complexed with 5- fluorouridine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TGV
- Type
- protein
- Length
- 492 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
- 5UD, K, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 34% helix, 28% strand | P12758 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 33% helix, 29% strand | P12758 |
Ligands and binding sites
- 5UD · 5-fluorouridine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · 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 | 306 | 0.65 | 0.81 | 44 | SO4, 5UD |
| 2 | 205 | 0.63 | 0.83 | 31 | SO4, 5UD |
| 3 | 111 | 0.40 | 0.75 | 19 | empty |
| 4 | 72 | 0.29 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2003 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1TGV · Structure of E. coli Uridine Phosphorylase complexed with 5-Fluorouridine and sulfate · 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 B 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 P12758
- Elsewhere: RCSB PDB 1TGV · PDBe 1TGV · UniProt P12758
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