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Crystal structure of varicella zoster virus thymidine kinase in complex with bvdu-mp and ADP
Analyse Crystal structure of varicella zoster virus thymidine kinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OSN
- Type
- protein
- Length
- 1,268 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- P0C0E6
- Ligands
- ADP, BVP
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 325 | 53% helix, 12% strand | P0C0E6 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 315 | 55% helix, 12% strand | P0C0E6 |
| C | Thymidine kinase (EC 2.7.1.21) | protein | 313 | 54% helix, 12% strand | P0C0E6 |
| D | Thymidine kinase (EC 2.7.1.21) | protein | 315 | 55% helix, 12% strand | P0C0E6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- BVP · (E)-5-(2-bromovinyl)-2'-deoxyuridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.86 | 0.87 | 113 | empty |
| 2 | 687 | 0.80 | 0.85 | 77 | empty |
| 3 | 706 | 0.80 | 0.84 | 80 | empty |
| 4 | 667 | 0.72 | 0.79 | 69 | ADP, BVP |
| 5 | 174 | 0.61 | 0.83 | 26 | BVP |
Interfaces
6 interfaces between chains.
- A–B · 1796 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1781 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 531 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 445 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 187 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1OSN · Crystal structure of Varicella zoster virus thymidine kinase in complex with BVDU-MP and… · 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 P0C0E6
- Elsewhere: RCSB PDB 1OSN · PDBe 1OSN · UniProt P0C0E6
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