Research workbench
X-ray structure of the thymidine phosphorylase from salmonella typhimurium in complex with uridine
Analyse X-ray structure of the thymidine phosphorylase from salmonella typhimurium in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YYY
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine phosphorylase
- EC
- 2.4.2.4
- UniProt
- Q7CP66
- Ligands
- URI
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidine phosphorylase (EC 2.4.2.4) | protein | 440 | 45% helix, 14% strand | Q7CP66 |
Ligands and binding sites
- URI · Uridine · ligand · 2 copies · chains B
- CIT · Citric acid · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.84 | 0.85 | 103 | CIT |
| 2 | 632 | 0.75 | 0.82 | 54 | URI, CIT |
| 3 | 106 | 0.66 | 0.90 | 29 | empty |
| 4 | 75 | 0.53 | 0.86 | 20 | empty |
| 5 | 107 | 0.43 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 677 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4YYY · X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7CP66 · AlphaFold monomer V2.0 prediction for thymidine phosphorylase (Q7CP66) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q7CP66
- Elsewhere: RCSB PDB 4YYY · PDBe 4YYY · UniProt Q7CP66
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