MolNFT v1 · #98713 · protein
Thymidine phosphorylase from E.COLI with 3'-azido-3'-deoxythymidine
4LHM: “Thymidine phosphorylase from E.COLI with 3'-azido-3'-deoxythymidine”. X-ray diffraction, 2 ligands (AZZ, SO4), 3 pockets (best druggability 0.74). MolNFT v1 #98713 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4LHM
- Type
- protein
- Length
- 440 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine phosphorylase
- EC
- 2.4.2.4
- UniProt
- P07650
- Ligands
- AZZ, SO4
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine phosphorylase (EC 2.4.2.4) | protein | 440 | 47% helix, 15% strand | P07650 |
Ligands and binding sites
- AZZ · 3'-azido-3'-deoxythymidine · ligand · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.74 | 0.83 | 45 | SO4, AZZ |
| 2 | 88 | 0.56 | 0.86 | 20 | empty |
| 3 | 56 | 0.30 | 0.76 | 11 | empty |
Compared structures
- 4LHM · Thymidine phosphorylase from E.coli with 3'-azido-3'-deoxythymidine · the same entry in another collection · chain A against A, TM-score 1.00
- P07650 · AlphaFold monomer V2.0 prediction for thymidine phosphorylase (P07650) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P07650
- Elsewhere: RCSB PDB 4LHM · PDBe 4LHM · UniProt P07650
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