MolNFT v1 · #12485 · protein
Crystal structure of thymidine kinase from herpes simplex virus type I complexed with 5-iododeoxyuridine
1KI7: “Crystal structure of thymidine kinase from herpes simplex virus type I complexed with 5-iododeoxyuridine”. X-ray diffraction, 2 ligands (ID2, SO4), 9 pockets (best druggability 0.78). MolNFT v1 #12485 on GenesisL1: 3D structure…
- PDB
- 1KI7
- Type
- protein
- Length
- 611 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
- ID2, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 302 | 53% helix, 13% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 309 | 56% helix, 13% strand | P03176 |
Ligands and binding sites
- ID2 · 5-iododeoxyuridine · 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.78 | 0.98 | 20 | ID2 |
| 2 | 235 | 0.71 | 0.87 | 36 | SO4, ID2 |
| 3 | 166 | 0.57 | 0.81 | 29 | empty |
| 4 | 110 | 0.47 | 0.79 | 21 | empty |
| 5 | 119 | 0.46 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1709 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1KI7 · Crystal structure of thymidine kinase from herpes simplex virus type I complexed 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 1KI7 · PDBe 1KI7 · UniProt P03176
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