Research workbench
Deoxyribonucleoside kinase
Analyse Deoxyribonucleoside kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YBH
- Type
- protein
- Length
- 1,284 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside kinase
- EC
- 2.7.1.145
- UniProt
- Q9XZT6
- Ligands
- 8LK, SO4
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 217 | 48% helix, 15% strand | Q9XZT6 |
| B | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 215 | 47% helix, 15% strand | Q9XZT6 |
| C | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 212 | 48% helix, 15% strand | Q9XZT6 |
| D | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 219 | 48% helix, 15% strand | Q9XZT6 |
| E | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 209 | 49% helix, 15% strand | Q9XZT6 |
| F | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 212 | 49% helix, 13% strand | Q9XZT6 |
Ligands and binding sites
- 8LK · Pyrrolo-dC · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 21 copies · chains A, C, B, D, E, F
- GOL · Glycerol · additive · 11 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.73 | 0.87 | 36 | 8LK, SO4 |
| 2 | 58 | 0.73 | 0.98 | 17 | GOL |
| 3 | 55 | 0.72 | 0.98 | 17 | empty |
| 4 | 370 | 0.72 | 0.83 | 42 | 8LK, SO4 |
| 5 | 53 | 0.72 | 0.98 | 16 | GOL |
Interfaces
8 interfaces between chains.
- A–C · 1457 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1454 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1375 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 398 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 113 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 6YBH · PDBe 6YBH · UniProt Q9XZT6
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