MolNFT v1 · #82653 · protein
Thymidine kinase from herpes simplex virus type 1 in complex with ADP and 5-iodo-deoxyuridine-monophosphate
3VTK: “Thymidine kinase from herpes simplex virus type 1 in complex with ADP and 5-iodo-deoxyuridine-monophosphate”. X-ray diffraction, 2 ligands (ADP, 5IU), 2 pockets (best druggability 0.72). MolNFT v1 #82653 on GenesisL1: 3D structure…
- PDB
- 3VTK
- Type
- protein
- Length
- 313 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- P03176
- Ligands
- ADP, 5IU
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 313 | 55% helix, 11% strand | P03176 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- 5IU · 5-iodo-2'-deoxyuridine-5'-monophosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.72 | 0.86 | 39 | ADP, 5IU |
| 2 | 69 | 0.35 | 0.77 | 16 | empty |
Compared structures
- 3VTK · Thymidine kinase from herpes simplex virus type 1 in complex with ADP and… · 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 3VTK · PDBe 3VTK · UniProt P03176
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