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Crystal structure of myristoylated K7C catalytic subunit of camp- dependent protein kinase in complex with SP20 and AMP-pnp
Analyse Crystal structure of myristoylated K7C catalytic subunit of camp- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DFX
- Type
- protein
- Length
- 370 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
- P05132, P63248
- Ligands
- MYR, ANP, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 350 | 38% helix, 15% strand | P05132 |
| I | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 30% helix, 10% strand | P63248 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains E
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains E, I
- MG · Magnesium ion · metal · 2 copies · chains E, I
- GOL · Glycerol · additive · 3 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.80 | 0.91 | 42 | ANP, MG |
| 2 | 183 | 0.57 | 0.80 | 26 | MYR |
| 3 | 55 | 0.35 | 0.79 | 14 | empty |
| 4 | 94 | 0.35 | 0.74 | 15 | empty |
| 5 | 61 | 0.29 | 0.74 | 13 | GOL |
Interfaces
1 interface between chains.
- E–I · 1024 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 lipid (phosphorylation, myristoylation).
Compared structures
- 4DFX · Crystal structure of myristoylated K7C catalytic subunit of cAMP-dependent protein kinase… · the same entry in another collection · chain E against E, 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 I against A, TM-score 0.40
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 P05132
- Every structure of UniProt P63248
- Elsewhere: RCSB PDB 4DFX · PDBe 4DFX · UniProt P05132 · UniProt P63248
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