Research workbench
Structure of E. COLI uridine phosphorylase complexed to 5- (PHENYLTHIO)ACYCLOURIDINE (ptau)
Analyse Structure of E. COLI uridine phosphorylase complexed to 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U1D
- Type
- protein
- Length
- 1,505 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P12758
- Ligands
- 181, K, PO4
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 253 | 34% helix, 28% strand | P12758 |
| B, E | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 28% strand | P12758 |
| C, D, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 33% helix, 28% strand | P12758 |
Ligands and binding sites
- 181 · 1-((2-hydroxyethoxy)methyl)-5-(phenylthio)pyrimidine-2,4(1H,3H)-dione · ligand · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 3 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.80 | 0.81 | 106 | empty |
| 2 | 364 | 0.72 | 0.84 | 43 | PO4, 181 |
| 3 | 363 | 0.70 | 0.83 | 38 | PO4, 181 |
| 4 | 307 | 0.70 | 0.84 | 31 | PO4, 181 |
| 5 | 348 | 0.70 | 0.83 | 41 | PO4, 181 |
Interfaces
12 interfaces between chains.
- A–B · 2147 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2120 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2114 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 1069 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 1057 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1U1D · Structure of e. coli uridine phosphorylase complexed to 5-(phenylthio)acyclouridine (ptau) · the same entry in another collection · chain F against F, 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 1U1D · PDBe 1U1D · UniProt P12758
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