MolNFT v1 · #102600 · protein
Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ara-edu
4OQM: “Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ara-edu”. X-ray diffraction, 2 ligands (FDU, SO4), 7 pockets (best druggability 0.79). MolNFT v1 #102600 on GenesisL1: 3D structure, binding…
- PDB
- 4OQM
- 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
- FDU, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 306 | 57% helix, 12% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 313 | 57% helix, 12% strand | P03176 |
Ligands and binding sites
- FDU · 1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, 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 | 106 | 0.79 | 0.99 | 20 | FDU |
| 2 | 269 | 0.65 | 0.82 | 38 | FDU, SO4 |
| 3 | 412 | 0.62 | 0.77 | 67 | empty |
| 4 | 104 | 0.49 | 0.81 | 21 | empty |
| 5 | 82 | 0.42 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1719 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4OQM · Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with… · 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 4OQM · PDBe 4OQM · UniProt P03176
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