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Crystal structure of myristoylated WT catalytic subunit of cAMP-dependent protein kinase in complex with SP20

Analyse Crystal structure of myristoylated WT 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: 4DG2
Type: protein
Length: 370 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Mus musculus; SYNTHETIC CONSTRUCT
Molecule: cAMP-dependent protein kinase catalytic subunit alpha; cAMP-dependent protein kinase…
EC: 2.7.11.11
UniProt: P05132, P63248
Ligands: MYR
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · resolution 2 · 2 distinct chains · 37% 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	37% 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

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	358	0.78	0.88	44	empty
2	218	0.57	0.79	29	MYR
3	112	0.44	0.78	20	empty
4	97	0.36	0.74	17	empty
5	57	0.31	0.76	18	empty

Interfaces

1 interface between chains.

E–I · 1004 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 1 lipid (phosphorylation, myristoylation).

Compared structures

4DG2 · Crystal structure of myristoylated wt catalytic subunit of camp- dependent protein kinase… · the same entry in another collection · chain E against E, TM-score 1.00
P05132 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain E against A, TM-score 0.98
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 4DG2 · PDBe 4DG2 · UniProt P05132 · UniProt P63248

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