MolNFT v1 · #29901 · protein
Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine
1ZMX · Deoxynucleoside kinase: “Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant in complex with thymidine”. X-ray diffraction, 2 ligands (THM, SO4), 16 pockets (best druggability 0.73). MolNFT v1 #29901 on…
- 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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