Research workbench
Crystal structure of the autoinhibited form of mouse DAPK2 in complex with AMP
Analyse Crystal structure of the autoinhibited form of mouse DAPK2 in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YAB
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 2
- EC
- 2.7.11.1
- UniProt
- Q8VDF3
- Ligands
- AMP, CA, SO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Death-associated protein kinase 2 (EC 2.7.11.1) | protein | 299 | 36% helix, 19% strand | Q8VDF3 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.80 | 0.88 | 62 | AMP, SO4 |
| 2 | 411 | 0.80 | 0.88 | 55 | SO4 |
| 3 | 120 | 0.63 | 0.87 | 22 | AMP |
| 4 | 70 | 0.43 | 0.81 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1362 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2YAB · Crystal structure of the autoinhibited form of mouse DAPK2 in complex with AMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VDF3 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 2 (Q8VDF3) · 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 Q8VDF3
- Elsewhere: RCSB PDB 2YAB · PDBe 2YAB · UniProt Q8VDF3
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