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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
- 1E2J
- Type
- protein
- Length
- 620 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
- THM, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 306 | 58% helix, 12% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 314 | 56% helix, 12% strand | P03176 |
Ligands and binding sites
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 | 138 | 0.81 | 0.98 | 24 | THM |
| 2 | 204 | 0.65 | 0.84 | 29 | SO4, THM |
| 3 | 175 | 0.56 | 0.81 | 31 | empty |
| 4 | 118 | 0.47 | 0.79 | 20 | empty |
| 5 | 92 | 0.44 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1725 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1E2J · 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 1E2J · PDBe 1E2J · UniProt P03176
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