MolNFT v1 · #111034 · protein
X-ray structure of the thymidine phosphorylase from salmonella typhimurium in complex with thymidine
4YEK: “X-ray structure of the thymidine phosphorylase from salmonella typhimurium in complex with thymidine”. X-ray diffraction, 2 ligands (THM, SO4), 10 pockets (best druggability 0.80). MolNFT v1 #111034 on GenesisL1: 3D structure…
- PDB
- 4YEK
- 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
- THM, SO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidine phosphorylase (EC 2.4.2.4) | protein | 440 | 46% helix, 15% strand | Q7CP66 |
Ligands and binding sites
- THM · Thymidine · ligand · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.80 | 0.88 | 54 | GOL |
| 2 | 843 | 0.75 | 0.79 | 60 | THM |
| 3 | 562 | 0.73 | 0.81 | 47 | SO4, THM |
| 4 | 58 | 0.70 | 0.97 | 24 | empty |
| 5 | 55 | 0.66 | 0.96 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 908 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4YEK · 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 0.96
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 4YEK · PDBe 4YEK · UniProt Q7CP66
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