Research workbench
Crystal structure of pka with compound 36
Analyse Crystal structure of pka with compound 36 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L9L
- Type
- protein
- Length
- 716 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- cAMP-dependent protein kinase catalytic subunit alpha; cAMP-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P17612, P61925
- Ligands
- L9L
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · resolution 2 · 4 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | cAMP-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 340 | 39% helix, 16% strand | P17612 |
| C | cAMP-dependent protein kinase inhibitor alpha | protein | 19 | 32% helix, 0% strand | P61925 |
| B | cAMP-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 339 | 38% helix, 16% strand | P17612 |
| D | cAMP-dependent protein kinase inhibitor alpha | protein | 18 | 33% helix, 0% strand | P61925 |
Ligands and binding sites
- L9L · 5-[2-({(2S)-2-amino-3-[4-(trifluoromethyl)phenyl]propyl}amino)-1,3-thiazol-5-yl]-1,3-dihydro-2H-indol-2-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.79 | 0.85 | 58 | L9L |
| 2 | 527 | 0.78 | 0.85 | 59 | L9L |
| 3 | 83 | 0.52 | 0.84 | 12 | empty |
| 4 | 92 | 0.49 | 0.81 | 16 | empty |
| 5 | 72 | 0.34 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 956 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 907 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3L9L · Crystal structure of PKA with compound 36 · the same entry in another collection · chain D against D, TM-score 1.00
- P17612 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P61925 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain D against A, TM-score 0.42
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 P17612
- Every structure of UniProt P61925
- Elsewhere: RCSB PDB 3L9L · PDBe 3L9L · UniProt P17612 · UniProt P61925
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