Research workbench
Crystal structure of the apo form of the unphosphorylated human death associated protein kinase 3 (DAPK3)
Analyse Crystal structure of the apo form of the unphosphorylated human death… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A6O
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- HOMO SAPIENS
- Molecule
- Death-associated protein kinase 3
- EC
- 2.7.11.1
- UniProt
- O43293
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.6 · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 265 | 38% helix, 20% strand | O43293 |
| B | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 266 | 37% helix, 20% strand | O43293 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.77 | 0.83 | 69 | GOL |
| 2 | 159 | 0.62 | 0.83 | 20 | GOL |
| 3 | 141 | 0.61 | 0.84 | 23 | GOL |
| 4 | 63 | 0.44 | 0.83 | 17 | empty |
| 5 | 144 | 0.40 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2287 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5A6O · Crystal structure of the apo form of the unphosphorylated human death associated protein… · the same entry in another collection · chain A against A, TM-score 1.00
- O43293 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 3 (O43293) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O43293
- Elsewhere: RCSB PDB 5A6O · PDBe 5A6O · UniProt O43293
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.