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The nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography
Analyse The nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E2I
- 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
- APS, ARP, SO4
- Pockets
- 10 · best druggability 0.79
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 | 300 | 56% helix, 13% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 313 | 56% helix, 12% strand | P03176 |
Ligands and binding sites
- APS · 9-hydroxypropyladenine, S-isomer · ligand · 2 copies · chains A, B
- ARP · 9-hydroxypropyladenine, R-isomer · 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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.79 | 0.98 | 18 | APS, ARP |
| 2 | 258 | 0.67 | 0.83 | 31 | SO4, APS, ARP |
| 3 | 207 | 0.55 | 0.79 | 32 | empty |
| 4 | 112 | 0.48 | 0.80 | 18 | empty |
| 5 | 94 | 0.44 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1757 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1E2I · The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray… · 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 1E2I · PDBe 1E2I · UniProt P03176
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