Research workbench
Crystal structure of thymidine kinase from herpes simplex virus type I complexed with 5-bromovinyldeoxyuridine
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
- 1KI8
- Type
- protein
- Length
- 613 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
- BVD, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 304 | 56% helix, 13% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 309 | 57% helix, 13% strand | P03176 |
Ligands and binding sites
- BVD · 5-bromovinyldeoxyuridine · 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 | 99 | 0.78 | 0.98 | 20 | BVD |
| 2 | 289 | 0.72 | 0.85 | 40 | SO4, BVD |
| 3 | 180 | 0.57 | 0.81 | 32 | empty |
| 4 | 137 | 0.48 | 0.79 | 23 | empty |
| 5 | 121 | 0.47 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1689 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1KI8 · 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 1KI8 · PDBe 1KI8 · UniProt P03176
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