Research workbench
Crystal structure of human zipper-interacting protein kinase (zipk, alias DAPK3) in complex with a PYRAZOLO[3,4-D]PYRIMIDINONE ligand (HS38)
Analyse Crystal structure of human zipper-interacting protein kinase (zipk, alias… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VJA
- Type
- protein
- Length
- 1,058 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 3
- EC
- 2.7.11.1
- UniProt
- O43293
- Ligands
- DUK, ILE
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 266 | 39% helix, 20% strand | O43293 |
| B | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 266 | 39% helix, 20% strand | O43293 |
| C | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 265 | 37% helix, 20% strand | O43293 |
| D | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 261 | 38% helix, 19% strand | O43293 |
Ligands and binding sites
- DUK · (2R)-2-{[1-(3-chlorophenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]sulfanyl}propanamide · ligand · 4 copies · chains A, B, C, D
- ILE · Isoleucine · ligand · chains D
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.66 | 0.78 | 42 | DUK |
| 2 | 373 | 0.66 | 0.79 | 38 | DUK |
| 3 | 377 | 0.64 | 0.78 | 41 | DUK |
| 4 | 391 | 0.64 | 0.78 | 40 | DUK |
| 5 | 306 | 0.58 | 0.77 | 31 | empty |
Interfaces
5 interfaces between chains.
- B–D · 814 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 796 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 74 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 67 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VJA · Crystal Structure of human zipper-interacting protein kinase (ZIPK, alias DAPK3) in… · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.98
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 5VJA · PDBe 5VJA · UniProt O43293
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