Research workbench
X-ray structure of the unliganded thymidine phosphorylase from salmonella typhimurium at 2.05 a resolution
Analyse X-ray structure of the unliganded thymidine phosphorylase from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XR5
- 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
- CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidine phosphorylase (EC 2.4.2.4) | protein | 440 | 47% helix, 15% strand | Q7CP66 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.75 | 0.81 | 52 | empty |
| 2 | 639 | 0.72 | 0.79 | 52 | empty |
| 3 | 61 | 0.68 | 0.96 | 24 | empty |
| 4 | 68 | 0.45 | 0.82 | 15 | empty |
| 5 | 57 | 0.44 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 937 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4XR5 · X-ray structure of the unliganded thymidine phosphorylase from Salmonella typhimurium at… · 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 0.99
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 4XR5 · PDBe 4XR5 · UniProt Q7CP66
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.