Research workbench
Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster multisubstrate deoxyribonucleoside kinase
Analyse Structural studies of nucleoside analog and feedback inhibitor binding to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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