MolNFT v1 · #17894 · protein
Crystal structure of HSV1-tk complexed with TP5A
1P7C · Thymidine kinase: “Crystal structure of HSV1-tk complexed with TP5A”. X-ray diffraction, 3 ligands (T5A, THM, SO4), 7 pockets (best druggability 0.76). MolNFT v1 #17894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1P7C
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- P03176
- Ligands
- T5A, THM, SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 301 | 55% helix, 13% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 318 | 55% helix, 12% strand | P03176 |
Ligands and binding sites
- T5A · P1-(5'-adenosyl)p5-(5'-thymidyl)pentaphosphate · ligand · chains A
- THM · Thymidine · ligand · chains B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.76 | 0.82 | 64 | T5A |
| 2 | 213 | 0.71 | 0.87 | 34 | SO4, THM |
| 3 | 146 | 0.55 | 0.82 | 25 | empty |
| 4 | 92 | 0.45 | 0.80 | 22 | empty |
| 5 | 74 | 0.34 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1725 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1P7C · Crystal Structure of HSV1-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 P03176
- Elsewhere: RCSB PDB 1P7C · PDBe 1P7C · UniProt P03176
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