1YDS: C-AMP-dependent protein kinase

Structure of CAMP-dependent protein kinase, alpha-catalytic subunit in complex with H8 protein kinase inhibitor [N-(2-methylamino)ethyl]-5-isoquinolinesulfonamide. Determined by X-ray diffraction at 2.2 Å resolution. Released 1 Apr 1997.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Bos taurus
Chains: 2
Atoms: 2,974
Mol. weight: 43.17 kDa
Ligands: IQS
Released: 1 Apr 1997

Explore 1YDS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YDS contains 19 α-helices and 13 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain E: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	16-31	16
α-helix	40-42	3
β-strand	43-51	9	1
β-strand	55-62	8	1
β-strand	67-75	9	1
α-helix	76-81	6
α-helix	85-97	13
β-strand	103	1	2
α-helix	104-105	2
β-strand	106-111	6	1
β-strand	115-121	7	1
β-strand	127	1	2
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	3
α-helix	169-171	3
β-strand	172-174	3	2
β-strand	180-182	3	2
β-strand	189-190	2	3
β-strand	195	1	4
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	4
α-helix	218-233	16
α-helix	243-252	10
α-helix	263-272	10
α-helix	289-292	4
α-helix	295-297	3
α-helix	302-306	5
α-helix	333-335	3

Chain I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	18-22	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-AMP-dependent protein kinase	E	protein	350	Bos taurus	P00517 (AlphaFold model)
Protein kinase inhibitor peptide	I	protein	20		P63249 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>1YDS_1 C-AMP-DEPENDENT PROTEIN KINASE (chains E)
GNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLV
KHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVM
EYVAGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYI
QVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFA
DQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKDGVNDIKNHKWFATT
DWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Sequence of entity 2 (I), FASTA

>1YDS_2 PROTEIN KINASE INHIBITOR PEPTIDE (chains I)
TTYADFIASGRTGRRNAIHD

Ligands and cofactors

ID	Name	Formula	Copies
IQS	N-[2-(methylamino)ethyl]-5-isoquinolinesulfonamide	C12 H15 N3 O2 S	1

Primary citation

Crystal structures of catalytic subunit of cAMP-dependent protein kinase in complex with isoquinolinesulfonyl protein kinase inhibitors H7, H8, and H89. Structural implications for selectivity. Engh, R.A., Girod, A., Kinzel, V. et al. J Biol Chem (1996) 271:26157-26164. DOI 10.1074/jbc.271.42.26157 · PubMed

Other PDB entries of the same protein (UniProt P00517 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4Z84 1.55 Å, PKAB3 in complex with pyrrolidine inhibitor 34a
4C38 1.58 Å, PKA-S6K1 Chimera with compound 21e (CCT239066) bound
1XH8 1.6 Å, Crystal Structures of Protein Kinase B Selective Inhibitors in Complex with Protein…
5VHB 1.61 Å, Crystal structure of Protein Kinase A in complex with the PKI peptide and…
1XH9 1.64 Å, Crystal Structures of Protein Kinase B Selective Inhibitors in Complex with Protein…
3ZO4 1.65 Å, The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors
4C33 1.7 Å, PKA-S6K1 Chimera Apo
4C37 1.7 Å, PKA-S6K1 Chimera with compound 21a (CCT196539) bound
8SF8 1.7 Å, Structure of bovine PKA bound to (R)-N-(4-(1H-pyrrolo[2,3-b]pyridin-4-yl)phenyl)-2-amino-…
4C34 1.78 Å, PKA-S6K1 Chimera with Staurosporine bound
3KKV 1.8 Å, Structure of PKA with a protein Kinase B-selective inhibitor.
4Z83 1.8 Å, PKAB3 in complex with pyrrolidine inhibitor 47a

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