Research workbench
X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target CAR26.
Analyse X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XX6
- Type
- protein
- Length
- 344 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Clostridium acetobutylicum
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- Q97F65
- Ligands
- ADP, ZN
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 178 | 22% helix, 31% strand | Q97F65 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 166 | 24% helix, 28% strand | Q97F65 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.56 | 0.89 | 19 | empty |
| 2 | 157 | 0.49 | 0.78 | 28 | ADP |
| 3 | 134 | 0.41 | 0.75 | 17 | empty |
| 4 | 124 | 0.41 | 0.75 | 18 | empty |
| 5 | 68 | 0.33 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1330 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 1XX6 · X-ray structure of clostridium acetobutylicum thymidine kinase with ADP. northeast… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97F65 · AlphaFold monomer V2.0 prediction for thymidine kinase (Q97F65) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q97F65
- Elsewhere: RCSB PDB 1XX6 · PDBe 1XX6 · UniProt Q97F65
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