MolNFT v1 · #12484 · protein
Crystal structure of thymidine kinase from herpes simplex virus type I complexed with a 5-iodouracil anhydrohexitol nucleoside
1KI6: “Crystal structure of thymidine kinase from herpes simplex virus type I complexed with a 5-iodouracil…”. X-ray diffraction, 2 ligands (AHU, SO4), 8 pockets (best druggability 0.79). MolNFT v1 #12484 on GenesisL1: 3D structure…
- PDB
- 1KI6
- Type
- protein
- Length
- 604 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
- AHU, SO4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 300 | 57% helix, 13% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 304 | 57% helix, 13% strand | P03176 |
Ligands and binding sites
- AHU · 1',5'-anhydro-2',3'-dideoxy-2'-(5-iodouracil-1-yl)-D-ababino-hexitol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.79 | 0.99 | 17 | AHU |
| 2 | 98 | 0.77 | 0.97 | 18 | AHU |
| 3 | 145 | 0.59 | 0.83 | 27 | empty |
| 4 | 101 | 0.47 | 0.80 | 20 | empty |
| 5 | 97 | 0.45 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1707 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1KI6 · Crystal structure of thymidine kinase from herpes simplex virus type I complexed with a… · 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 1KI6 · PDBe 1KI6 · UniProt P03176
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