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Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with compound 2
Analyse Crystal structure of human death associated protein kinase 3 (DAPK3) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A6N
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- 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
- U7E
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 271 | 39% helix, 20% strand | O43293 |
| B | Death-associated protein kinase 3 (EC 2.7.11.1) | protein | 267 | 37% helix, 20% strand | O43293 |
Ligands and binding sites
- U7E · 5-(3-sulfamoylphenyl)-1H-1,2,3,4-tetrazol-1-ide · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.83 | 0.84 | 108 | U7E |
| 2 | 192 | 0.61 | 0.81 | 22 | GOL |
| 3 | 220 | 0.47 | 0.74 | 30 | empty |
| 4 | 56 | 0.34 | 0.78 | 11 | empty |
| 5 | 61 | 0.31 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2292 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5A6N · Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with… · 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 0.92
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 5A6N · PDBe 5A6N · UniProt O43293
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