3IDB: PDB entry 3IDB

Crystal structure of (108-268)RIIb:C holoenzyme of cAMP-dependent protein kinase. Determined by X-ray diffraction at 1.62 Å resolution. Released 29 Sept 2009.

Method: X-ray diffraction
Resolution: 1.62 Å
Organisms: Mus musculus, Rattus norvegicus
Chains: 2
Atoms: 4,357
Mol. weight: 59.65 kDa
Ligands: MN, ANP
Released: 29 Sept 2009

Explore 3IDB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3IDB contains 26 α-helices and 23 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: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	16-30	15
α-helix	40-42	3
β-strand	43-51	9	1
β-strand	56-62	7	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
β-strand	199-200	2	5
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	311-312	2
α-helix	345-347	3

Chain B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	109-112	4
β-strand	113-114	2	5
α-helix	137-147	11
α-helix	151-154	4
α-helix	158-167	10
α-helix	168	1
β-strand	169-173	5	6
β-strand	178-180	3	7
β-strand	188-194	7	6
β-strand	196-203	8	7
β-strand	206-214	9	7
β-strand	218-219	2	6
α-helix	221-224	4
β-strand	233-236	4	7
β-strand	240-246	7	6
α-helix	247-259	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-dependent protein kinase catalytic subunit alpha	A	protein	350	Mus musculus	P05132 (AlphaFold model)
cAMP-dependent protein kinase type II-beta regulatory subunit	B	protein	161	Rattus norvegicus	P12369 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3IDB_1 cAMP-dependent protein kinase catalytic subunit alpha (chains A)
GNAAAAKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLV
KHKESGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVM
EYVAGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYI
QVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFA
DQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATT
DWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF

Sequence of entity 2 (B), FASTA

>3IDB_2 cAMP-dependent protein kinase type II-beta regulatory subunit (chains B)
TRRASVCAEAYNPDEEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDA
MFEKLVKEGEHVIDQGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGELALMYN
TPRAATITATSPGALWGLDRVTFRRIIVKNNAKKRKMYESF

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Primary citation

Novel isoform-specific interfaces revealed by PKA RIIbeta holoenzyme structures. Brown, S.H., Wu, J., Kim, C. et al. J Mol Biol (2009) 393:1070-1082. DOI 10.1016/j.jmb.2009.09.014 · PubMed

Other PDB entries of the same protein (UniProt P05132 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RDQ 1.26 Å, Hydrolysis of ATP in the crystal of Y204A mutant of cAMP-dependent protein kinase
4DFX 1.35 Å, Crystal structure of myristoylated K7C catalytic subunit of cAMP-dependent protein…
4HPU 1.55 Å, Crystal structure of the catalytic subunit of cAMP-dependent protein kinase displaying…
4IAI 1.55 Å, X-ray Structure of cAMP dependent protein kinase A in complex with high Ca2+…
9PC1 1.55 Å, Co-crystal structure of the cAMP-dependent protein kinase catalytic subunit alpha with…
3FJQ 1.6 Å, Crystal structure of cAMP-dependent protein kinase catalytic subunit alpha in complex…
4IAK 1.6 Å, Low temperature X-ray structure of cAMP dependent protein kinase A in complex with high…
4IB1 1.63 Å, Structure of cAMP dependent protein kinase A in complex with high K+ concentration, ADP…
7V0G 1.63 Å, Structure of cAMP-dependent protein kinase using a MD-MX procedure, produced using 1.63…
3QAL 1.7 Å, Crystal Structure of Arg280Ala mutant of Catalytic subunit of cAMP-dependent Protein…
3X2W 1.7 Å, Michaelis complex of cAMP-dependent Protein Kinase Catalytic Subunit
4O22 1.7 Å, Binary complex of metal-free PKAc with SP20.

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