5M6Y: PDB entry 5M6Y

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a methylisoquinoline Fasudil-derivative. Determined by X-ray diffraction at 1.37 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 1.37 Å
Organisms: Cricetulus griseus, Homo sapiens
Chains: 2
Atoms: 3,591
Mol. weight: 43.76 kDa
Ligands: 7KB
Released: 6 Jun 2018

Explore 5M6Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M6Y contains 20 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 A: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-31	30
α-helix	40-42	3
β-strand	43-52	10	1
β-strand	55-62	8	1
β-strand	68-75	8	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	243-251	9
α-helix	263-272	10
α-helix	277-279	3
α-helix	289-292	4
α-helix	295-297	3
α-helix	302-306	5
α-helix	311-312	2

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	18-21	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-dependent protein kinase catalytic subunit alpha	A	protein	353	Cricetulus griseus	P25321 (AlphaFold model)
cAMP-dependent protein kinase inhibitor alpha	B	protein	20	Homo sapiens	P61925 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5M6Y_1 cAMP-dependent protein kinase catalytic subunit alpha (chains A)
GHMGNAAAAKKGSEQESVKEFLAKAKEEFLKKWESPSQNTAQLDHFDRIKTLGTGSFGRV
MLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLY
MVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQ
GYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPP
FFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWF
ATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF

Sequence of entity 2 (B), FASTA

>5M6Y_2 cAMP-dependent protein kinase inhibitor alpha (chains B)
TTYADFIASGRTGRRNAIHD

Ligands and cofactors

ID	Name	Formula	Copies
7KB	5-(1,4-diazepan-1-ylsulfonyl)-4-methyl-isoquinoline	C15 H19 N3 O2 S	1

Water and common crystallization additives (MPD) are not listed.

Primary citation

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with differently methylated Fasudil-derived ligands. Wienen-Schmidt, B., Jonker, H., Gerber, H.-D. et al. To be published.

Other PDB entries of the same protein (UniProt P25321 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5N1F 1.12 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
5N3J 1.12 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
4WIH 1.14 Å, Crystal structure of cAMP-dependent Protein Kinase A from Cricetulus griseus
5N1G 1.14 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
5N3I 1.14 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
5N3S 1.14 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
5N3G 1.16 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
5N1H 1.18 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
9REC 1.2 Å, Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in…
5N3T 1.21 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
5N3N 1.22 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…
5N3M 1.23 Å, cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like…

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