MolNFT v1 · #41300 · protein
Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster multisubstrate deoxyribonucleoside kinase
2JJ8 · Deoxynucleoside kinase: “Structural studies of nucleoside analog and feedback inhibitor binding to drosophila melanogaster…”. X-ray diffraction, 2 ligands (AZZ, SO4), 7 pockets (best druggability 0.58). MolNFT v1 #41300 on…
- PDB
- 2JJ8
- Type
- protein
- Length
- 736 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
- AZZ, SO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 184 | 52% helix, 17% strand | Q9XZT6 |
| B, D | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 186 | 53% helix, 17% strand | Q9XZT6 |
| C | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 180 | 54% helix, 18% strand | Q9XZT6 |
Ligands and binding sites
- AZZ · 3'-azido-3'-deoxythymidine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.58 | 0.77 | 36 | SO4, AZZ |
| 2 | 221 | 0.57 | 0.79 | 33 | SO4, AZZ |
| 3 | 204 | 0.52 | 0.77 | 27 | SO4, AZZ |
| 4 | 148 | 0.48 | 0.77 | 30 | SO4, AZZ |
| 5 | 95 | 0.46 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1511 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1508 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2JJ8 · 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 C 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 2JJ8 · PDBe 2JJ8 · UniProt Q9XZT6
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