Research workbench
Crystal structure of camp-dependent protein kinase (PKA) in complex with short-chain fasudil-derivative N-(2-AMINOETHYL)ISOQUINOLINE-5- sulfonamide (soaked)
Analyse Crystal structure of camp-dependent protein kinase (PKA) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YNB
- Type
- protein
- Length
- 361 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
- IQU
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 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 | 348 | 40% helix, 15% strand | P25321 |
| B | Camp-dependent protein kinase inhibitor alpha | protein | 13 | 0% helix, 8% strand | P63248 |
Ligands and binding sites
- IQU · N-(2-aminoethyl)isoquinoline-5-sulfonamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.78 | 0.86 | 43 | IQU |
| 2 | 268 | 0.60 | 0.79 | 42 | DMS |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6YNB · Crystal structure of cAMP-dependent Protein Kinase (PKA) in complex with short-chain… · 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 0.22
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 6YNB · PDBe 6YNB · UniProt P25321 · UniProt P63248
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