MolNFT v1 · #52037 · protein
Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster multisubstrate deoxyribonucleoside kinase
2VP2 · Deoxynucleoside kinase: “Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster…”. X-ray diffraction, 1 ligand (DGT), 6 pockets (best druggability 0.75). MolNFT v1 #52037 on GenesisL1: 3D…
- PDB
- 2VP2
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside kinase
- EC
- 2.7.1.145
- UniProt
- Q9XZT6
- Ligands
- DGT
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 198 | 49% helix, 15% strand | Q9XZT6 |
| B | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 197 | 51% helix, 16% strand | Q9XZT6 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.75 | 0.92 | 31 | DGT |
| 2 | 200 | 0.71 | 0.88 | 40 | DGT |
| 3 | 89 | 0.48 | 0.81 | 15 | empty |
| 4 | 75 | 0.44 | 0.80 | 12 | empty |
| 5 | 81 | 0.39 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1473 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2VP2 · Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XZT6 · AlphaFold monomer V2.0 prediction for deoxynucleoside kinase (Q9XZT6) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 2VP2 · PDBe 2VP2 · UniProt Q9XZT6
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