Research workbench
Crystal structure of drosophila deoxyribonucleoside kinase in complex with dttp
Analyse Crystal structure of drosophila deoxyribonucleoside kinase in complex with dttp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OE0
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- DROSOPHILA MELANOGASTER
- Molecule
- Deoxyribonucleoside kinase
- EC
- 2.7.1.145
- UniProt
- Q9XZT6
- Ligands
- TTP, MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Deoxyribonucleoside kinase (EC 2.7.1.145) | protein | 198 | 50% helix, 15% strand | Q9XZT6 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.76 | 0.93 | 31 | TTP, MG |
| 2 | 969 | 0.76 | 0.79 | 99 | TTP, MG |
| 3 | 923 | 0.75 | 0.79 | 94 | TTP |
| 4 | 160 | 0.74 | 0.92 | 30 | TTP, MG |
| 5 | 106 | 0.48 | 0.80 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1475 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1458 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 535 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 529 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OE0 · Crystal structure of drosophila deoxyribonucleoside kinase in complex with dttp · the same entry in another collection · chain D against D, TM-score 1.00
- Q9XZT6 · AlphaFold monomer V2.0 prediction for deoxynucleoside kinase (Q9XZT6) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9XZT6
- Elsewhere: RCSB PDB 1OE0 · PDBe 1OE0 · UniProt Q9XZT6
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