Research workbench
Crystal structure of drosophila deoxyribonucleotide kinase complexed with the substrate deoxythymidine
Analyse Crystal structure of drosophila deoxyribonucleotide kinase complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OT3
- Type
- protein
- Length
- 1,545 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribonucleoside kinase
- EC
- 2.7.1.145
- UniProt
- Q9XZT6
- Ligands
- THM, SO4
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Deoxyribonucleoside kinase (EC 2.7.1.145) | protein | 197 | 49% helix, 14% strand | Q9XZT6 |
| B, E, F, G, H | Deoxyribonucleoside kinase (EC 2.7.1.145) | protein | 192 | 53% helix, 16% strand | Q9XZT6 |
| D | Deoxyribonucleoside kinase (EC 2.7.1.145) | protein | 191 | 51% helix, 15% strand | Q9XZT6 |
Ligands and binding sites
- THM · Thymidine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 9 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
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.70 | 0.86 | 32 | SO4, THM |
| 2 | 197 | 0.70 | 0.87 | 34 | SO4, THM |
| 3 | 207 | 0.70 | 0.87 | 38 | SO4, THM |
| 4 | 157 | 0.69 | 0.89 | 36 | SO4, THM |
| 5 | 203 | 0.67 | 0.85 | 36 | SO4, THM |
Interfaces
5 interfaces between chains.
- A–B · 1443 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1434 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1428 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1412 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OT3 · Crystal structure of Drosophila deoxyribonucleotide kinase complexed with the substrate… · 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 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 1OT3 · PDBe 1OT3 · UniProt Q9XZT6
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