Research workbench
Herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9A resolution
Analyse Herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KI5
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (thymidine kinase)
- EC
- 2.7.1.21
- UniProt
- P03176
- Ligands
- AC2, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (thymidine kinase) (EC 2.7.1.21) | protein | 300 | 56% helix, 13% strand | P03176 |
| B | Protein (thymidine kinase) (EC 2.7.1.21) | protein | 304 | 56% helix, 13% strand | P03176 |
Ligands and binding sites
- AC2 · 9-hyroxyethoxymethylguanine · 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
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 | 131 | 0.80 | 0.97 | 18 | AC2 |
| 2 | 101 | 0.78 | 0.97 | 18 | AC2 |
| 3 | 192 | 0.63 | 0.84 | 39 | empty |
| 4 | 127 | 0.50 | 0.80 | 22 | empty |
| 5 | 122 | 0.47 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1752 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2KI5 · Herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9A… · 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 2KI5 · PDBe 2KI5 · UniProt P03176
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