Research workbench
Crystal structure of the camp-dependent protein kinase a cocrystallized with N,N-dimethylisoquinoline-5-sulfonamide and pki (5-24)
Analyse Crystal structure of the camp-dependent protein kinase a cocrystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YOT
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Camp-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P25321, P63248
- Ligands
- P4W
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 353 | 39% helix, 15% strand | P25321 |
| B | Camp-dependent protein kinase inhibitor alpha | protein | 19 | 37% helix, 0% strand | P63248 |
Ligands and binding sites
- P4W · ~{N},~{N}-dimethylisoquinoline-5-sulfonamide · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.77 | 0.84 | 44 | P4W |
| 2 | 188 | 0.58 | 0.81 | 24 | P4W |
| 3 | 111 | 0.38 | 0.74 | 21 | empty |
| 4 | 72 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 822 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 6YOT · Crystal structure of the cAMP-dependent protein kinase A cocrystallized with… · the same entry in another collection · chain A against A, TM-score 1.00
- P63248 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain B against A, TM-score 0.38
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 P25321
- Every structure of UniProt P63248
- Elsewhere: RCSB PDB 6YOT · PDBe 6YOT · UniProt P25321 · UniProt P63248
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