MolNFT v1 · #55114 · protein
Crystal structure of the autoinhibited form of mouse DAPK2 in complex with ATP
2YAA · Death-associated protein kinase 2: “Crystal structure of the autoinhibited form of mouse DAPK2 in complex with ATP”. X-ray diffraction, 3 ligands (ATP, CA, SO4), 4 pockets (best druggability 0.81). MolNFT v1 #55114 on GenesisL1: 3D…
- PDB
- 2YAA
- Type
- protein
- Length
- 599 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
- ATP, CA, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 2 (EC 2.7.11.1) | protein | 300 | 36% helix, 18% strand | Q8VDF3 |
| B | Death-associated protein kinase 2 (EC 2.7.11.1) | protein | 299 | 38% helix, 18% strand | Q8VDF3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 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 | 519 | 0.81 | 0.88 | 82 | ATP |
| 2 | 322 | 0.76 | 0.87 | 49 | empty |
| 3 | 93 | 0.61 | 0.87 | 21 | ATP |
| 4 | 158 | 0.43 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1326 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2YAA · Crystal structure of the autoinhibited form of mouse DAPK2 in complex with ATP · 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 B 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 2YAA · PDBe 2YAA · UniProt Q8VDF3
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