MolNFT v1 · #17888 · protein
Crystal structure of EHV4-tk complexed with TP5A
1P75 · Thymidine kinase: “Crystal structure of EHV4-tk complexed with TP5A”. X-ray diffraction, 2 ligands (T5A, SO4), 15 pockets (best druggability 0.69). MolNFT v1 #17888 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1P75
- Type
- protein
- Length
- 1,322 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
- T5A, SO4
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 331 | 49% helix, 14% strand | P24425 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 333 | 52% helix, 12% strand | P24425 |
| C | Thymidine kinase (EC 2.7.1.21) | protein | 330 | 52% helix, 15% strand | P24425 |
| D | Thymidine kinase (EC 2.7.1.21) | protein | 328 | 52% helix, 12% strand | P24425 |
Ligands and binding sites
- T5A · P1-(5'-adenosyl)p5-(5'-thymidyl)pentaphosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.69 | 0.81 | 36 | empty |
| 2 | 235 | 0.66 | 0.84 | 27 | empty |
| 3 | 465 | 0.65 | 0.77 | 53 | T5A |
| 4 | 368 | 0.64 | 0.79 | 41 | T5A |
| 5 | 314 | 0.63 | 0.79 | 34 | T5A |
Interfaces
3 interfaces between chains.
- C–D · 2100 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1941 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 803 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1P75 · Crystal structure of EHV4-TK complexed with TP5A · 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 1P75 · PDBe 1P75 · UniProt P24425
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