Research workbench
Crystal structure of thymidine kinase from herpes simplex virus type I complexed with deoxythymidine
Analyse Crystal structure of thymidine kinase from herpes simplex virus type I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KIM
- 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
- Ligands
- THM, SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 300 | 58% helix, 13% strand | — |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 304 | 58% helix, 13% strand | — |
Ligands and binding sites
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 | 94 | 0.76 | 0.97 | 18 | THM |
| 2 | 132 | 0.75 | 0.94 | 30 | SO4, THM |
| 3 | 149 | 0.58 | 0.83 | 27 | empty |
| 4 | 110 | 0.46 | 0.79 | 22 | empty |
| 5 | 100 | 0.46 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1722 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1KIM · 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
- Elsewhere: RCSB PDB 1KIM · PDBe 1KIM
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