Research workbench
Crystal structure of DAPK2 S308A CALCIUM/CALMODULIN complex
Analyse Crystal structure of DAPK2 S308A CALCIUM/CALMODULIN complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PAW
- Type
- protein
- Length
- 1,596 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 2; Calmodulin-1
- EC
- 2.7.11.1
- UniProt
- Q9UIK4, P0DP23
- Ligands
- CA
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Death-associated protein kinase 2 (EC 2.7.11.1) | protein | 316 | 40% helix, 17% strand | Q9UIK4 |
| D | Calmodulin-1 | protein | 145 | 61% helix, 3% strand | P0DP23 |
| E | Death-associated protein kinase 2 (EC 2.7.11.1) | protein | 305 | 40% helix, 18% strand | Q9UIK4 |
| F | Death-associated protein kinase 2 (EC 2.7.11.1) | protein | 314 | 41% helix, 17% strand | Q9UIK4 |
| G | Calmodulin-1 | protein | 67 | 55% helix, 3% strand | P0DP23 |
| H | Calmodulin-1 | protein | 54 | 63% helix, 0% strand | P0DP23 |
| C | Calmodulin-1 | protein | 79 | 65% helix, 3% strand | P0DP23 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains D, G, H, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.84 | 0.85 | 77 | empty |
| 2 | 584 | 0.80 | 0.85 | 64 | empty |
| 3 | 1005 | 0.78 | 0.80 | 90 | empty |
| 4 | 483 | 0.78 | 0.85 | 55 | empty |
| 5 | 467 | 0.76 | 0.84 | 56 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1845 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1319 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1239 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1206 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 923 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6PAW · Crystal structure of DAPK2 S308A Calcium/Calmodulin complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q9UIK4 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 2 (Q9UIK4) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 Q9UIK4
- Every structure of UniProt P0DP23
- Elsewhere: RCSB PDB 6PAW · PDBe 6PAW · UniProt Q9UIK4 · UniProt P0DP23
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