MolNFT v1 · #52096 · protein
Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster multisubstrate deoxyribonucleoside kinase
2VQS · Deoxynucleoside kinase: “Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster…”. X-ray diffraction, 2 ligands (BVD, SO4), 9 pockets (best druggability 0.61). MolNFT v1 #52096 on…
- PDB
- 2VQS
- Type
- protein
- Length
- 739 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside kinase
- EC
- 2.7.1.145
- UniProt
- Q9XZT6
- Ligands
- BVD, SO4
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 182 | 51% helix, 17% strand | Q9XZT6 |
| B | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 188 | 52% helix, 17% strand | Q9XZT6 |
| C | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 186 | 52% helix, 17% strand | Q9XZT6 |
| D | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 183 | 51% helix, 17% strand | Q9XZT6 |
Ligands and binding sites
- BVD · 5-bromovinyldeoxyuridine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.61 | 0.80 | 32 | SO4, BVD |
| 2 | 200 | 0.60 | 0.81 | 33 | SO4, BVD |
| 3 | 155 | 0.56 | 0.81 | 26 | SO4, BVD |
| 4 | 143 | 0.55 | 0.81 | 27 | SO4, BVD |
| 5 | 67 | 0.45 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1478 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1469 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 150 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VQS · Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila… · 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 0.98
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 2VQS · PDBe 2VQS · UniProt Q9XZT6
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