Research workbench
Crystal structure of DAPK1 catalytic domain in complex with the hinge binding fragment phthalazine
Analyse Crystal structure of DAPK1 catalytic domain in complex with the hinge binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YO4
- Type
- protein
- Length
- 280 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 1
- EC
- 2.7.11.1
- UniProt
- P53355
- Ligands
- 4FT, CL, SO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 1 (EC 2.7.11.1) | protein | 280 | 36% helix, 20% strand | P53355 |
Ligands and binding sites
- 4FT · phthalazine · ligand · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.71 | 0.79 | 63 | CL, 4FT |
| 2 | 80 | 0.38 | 0.77 | 19 | empty |
Compared structures
- 4YO4 · Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment… · the same entry in another collection · chain A against A, TM-score 1.00
- P53355 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 1 (P53355) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P53355
- Elsewhere: RCSB PDB 4YO4 · PDBe 4YO4 · UniProt P53355
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.