Research workbench
X-ray structure thymidine phosphorylase from salmonella typhimurium complex with SO4 at 2.19 a
Analyse X-ray structure thymidine phosphorylase from salmonella typhimurium complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X46
- 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
- SO4
- Pockets
- 10 · best druggability 0.77
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
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.77 | 0.85 | 62 | empty |
| 2 | 969 | 0.77 | 0.79 | 82 | EDO, SO4 |
| 3 | 472 | 0.73 | 0.82 | 49 | SO4 |
| 4 | 51 | 0.67 | 0.97 | 25 | empty |
| 5 | 54 | 0.61 | 0.93 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 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 4X46 · PDBe 4X46 · UniProt Q7CP66
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