MolNFT v1 · #17886 · protein
Crystal structure of EHV4-tk complexed with TP4A
1P73 · Thymidine kinase: “Crystal structure of EHV4-tk complexed with TP4A”. X-ray diffraction, 2 ligands (4TA, SO4), 12 pockets (best druggability 0.68). MolNFT v1 #17886 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1P73
- Type
- protein
- Length
- 1,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- P24425
- Ligands
- 4TA, SO4
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 320 | 49% helix, 13% strand | P24425 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 329 | 52% helix, 13% strand | P24425 |
| C | Thymidine kinase (EC 2.7.1.21) | protein | 317 | 50% helix, 14% strand | P24425 |
| D | Thymidine kinase (EC 2.7.1.21) | protein | 326 | 49% helix, 12% strand | P24425 |
Ligands and binding sites
- 4TA · P1-(5'-adenosyl)p4-(5'-(2'-deoxy-thymidyl))tetraphosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.68 | 0.80 | 36 | SO4 |
| 2 | 360 | 0.68 | 0.81 | 35 | empty |
| 3 | 466 | 0.67 | 0.78 | 41 | 4TA |
| 4 | 544 | 0.67 | 0.77 | 44 | 4TA |
| 5 | 312 | 0.65 | 0.80 | 37 | 4TA |
Interfaces
2 interfaces between chains.
- A–B · 1905 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1855 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1P73 · Crystal structure of EHV4-TK complexed with TP4A · 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 1P73 · PDBe 1P73 · UniProt P24425
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.