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Crystal structure of D. melanogaster deoxyribonucleoside kinase mutant N64D in complex with dttp
Analyse Crystal structure of D. melanogaster deoxyribonucleoside kinase mutant N64D in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZM7
- Type
- protein
- Length
- 790 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
- TTP, MG
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 197 | 51% helix, 16% strand | Q9XZT6 |
| B, C | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 198 | 51% helix, 16% strand | Q9XZT6 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.77 | 0.94 | 32 | TTP |
| 2 | 956 | 0.76 | 0.79 | 84 | TTP |
| 3 | 928 | 0.76 | 0.79 | 89 | MG, TTP |
| 4 | 162 | 0.74 | 0.92 | 32 | TTP |
| 5 | 59 | 0.44 | 0.82 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1484 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1467 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 529 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 526 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 54 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1ZM7 · Crystal structure of D. melanogaster deoxyribonucleoside kinase mutant N64D in complex… · 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 A against A, TM-score 0.99
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 1ZM7 · PDBe 1ZM7 · UniProt Q9XZT6
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