Research workbench
Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine
Analyse Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZMX
- Type
- protein
- Length
- 1,502 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
- THM, SO4
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 190 | 51% helix, 17% strand | Q9XZT6 |
| B, D | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 185 | 52% helix, 17% strand | Q9XZT6 |
| C | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 191 | 51% helix, 17% strand | Q9XZT6 |
| F | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 187 | 52% helix, 17% strand | Q9XZT6 |
| G | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 189 | 51% helix, 17% strand | Q9XZT6 |
| H | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 185 | 52% helix, 17% strand | Q9XZT6 |
Ligands and binding sites
- THM · Thymidine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 8 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
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.73 | 0.77 | 73 | SO4, THM |
| 2 | 808 | 0.70 | 0.76 | 71 | SO4, THM |
| 3 | 641 | 0.69 | 0.78 | 69 | empty |
| 4 | 312 | 0.63 | 0.80 | 34 | SO4, THM |
| 5 | 193 | 0.63 | 0.83 | 30 | SO4, THM |
Interfaces
12 interfaces between chains.
- C–D · 1467 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1454 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1447 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 1428 Ų buried · 9 hydrogen bonds · protein-protein
- F–H · 360 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1ZMX · Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex… · 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 1ZMX · PDBe 1ZMX · UniProt Q9XZT6
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