Research workbench
Cocrystal structure of camp-dependent protein kinase (PKA) in complex with a (S)-methyl substitued fasudil-derivative
Analyse Cocrystal structure of camp-dependent protein kinase (PKA) in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M75
- 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, P61925
- Ligands
- 9K6
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% 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 | 40% helix, 15% strand | P25321 |
| B | Camp-dependent protein kinase inhibitor alpha | protein | 19 | 42% helix, 0% strand | P61925 |
Ligands and binding sites
- 9K6 · 5-[[(2~{S})-2-methyl-1,4-diazepan-1-yl]sulfonyl]isoquinoline · 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
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 | 403 | 0.79 | 0.88 | 41 | 9K6 |
| 2 | 115 | 0.57 | 0.84 | 20 | DMS |
| 3 | 90 | 0.36 | 0.75 | 20 | empty |
| 4 | 59 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 5M75 · Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a (S)-methyl… · the same entry in another collection · chain A against A, TM-score 1.00
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 P61925
- Elsewhere: RCSB PDB 5M75 · PDBe 5M75 · UniProt P25321 · UniProt P61925
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