MolNFT v1 · #118311 · protein
X-ray structure of the thymidine phosphorylase from salmonella typhimurium in complex with cytidine and sulphate
5EY3: “X-ray structure of the thymidine phosphorylase from salmonella typhimurium in complex with cytidine and…”. X-ray diffraction, 2 ligands (CTN, SO4), 8 pockets (best druggability 0.84). MolNFT v1 #118311 on GenesisL1: 3D structure…
- PDB
- 5EY3
- Type
- protein
- Length
- 882 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
- CTN, SO4
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine phosphorylase (EC 2.4.2.4) | protein | 442 | 48% helix, 14% strand | Q7CP66 |
| B | Thymidine phosphorylase (EC 2.4.2.4) | protein | 440 | 47% helix, 14% strand | Q7CP66 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.84 | 0.86 | 89 | SO4, CTN |
| 2 | 551 | 0.72 | 0.80 | 45 | SO4 |
| 3 | 68 | 0.61 | 0.91 | 27 | empty |
| 4 | 85 | 0.47 | 0.82 | 19 | empty |
| 5 | 100 | 0.44 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5EY3 · 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 B against A, TM-score 0.98
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 5EY3 · PDBe 5EY3 · UniProt Q7CP66
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