MolNFT v1 · #17885 · protein
Crystal structure of EHV4-tk complexed with thy and ADP
1P72 · Thymidine kinase: “Crystal structure of EHV4-tk complexed with thy and ADP”. X-ray diffraction, 3 ligands (ADP, THM, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #17885 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1P72
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- P24425
- Ligands
- ADP, THM, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 323 | 51% helix, 14% strand | P24425 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 330 | 50% helix, 13% strand | P24425 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- THM · Thymidine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, 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 | 316 | 0.70 | 0.84 | 46 | ADP, THM |
| 2 | 364 | 0.70 | 0.82 | 29 | SO4 |
| 3 | 366 | 0.65 | 0.79 | 48 | ADP, THM |
| 4 | 55 | 0.27 | 0.74 | 15 | empty |
| 5 | 53 | 0.27 | 0.74 | 16 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1956 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1P72 · Crystal structure of EHV4-TK complexed with Thy and ADP · the same entry in another collection · 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 P24425
- Elsewhere: RCSB PDB 1P72 · PDBe 1P72 · UniProt P24425
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