MolNFT v1 · #52041 · protein
Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster multisubstrate deoxyribonucleoside kinase
2VP6 · Deoxynucleoside kinase: “Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster…”. X-ray diffraction, 2 ligands (5FU, SO4), 14 pockets (best druggability 0.67). MolNFT v1 #52041 on…
- PDB
- 2VP6
- Type
- protein
- Length
- 1,545 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside kinase
- EC
- 2.7.1.145
- UniProt
- Q9XZT6
- Ligands
- 5FU, SO4
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 197 | 49% helix, 16% strand | Q9XZT6 |
| B, E, F, G, H | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 192 | 51% helix, 16% strand | Q9XZT6 |
| D | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 191 | 53% helix, 16% strand | Q9XZT6 |
Ligands and binding sites
- 5FU · 5-fluoro-uridine-5'-monophosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.67 | 0.83 | 42 | SO4, 5FU |
| 2 | 179 | 0.66 | 0.86 | 34 | SO4, 5FU |
| 3 | 201 | 0.65 | 0.84 | 37 | SO4, 5FU |
| 4 | 182 | 0.65 | 0.85 | 36 | SO4, 5FU |
| 5 | 266 | 0.64 | 0.82 | 40 | SO4, 5FU |
Interfaces
5 interfaces between chains.
- E–F · 1484 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 1479 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1454 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1444 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VP6 · Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila… · the same entry in another collection · chain H against H, 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 2VP6 · PDBe 2VP6 · UniProt Q9XZT6
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