3E8C: Kinase domain of PKA

Crystal structures of the kinase domain of PKA in complex with ATP-competitive inhibitors. Determined by X-ray diffraction at 2.2 Å resolution. Released 18 Nov 2008.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Bos taurus
Chains: 12
Atoms: 18,893
Mol. weight: 260.85 kDa
Ligands: G96
Released: 18 Nov 2008

Explore 3E8C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3E8C contains 133 α-helices and 84 β-strands across 12 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: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
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	115-120	6	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	277-279	3
α-helix	289-292	4
α-helix	295-297	3
α-helix	302-306	5
α-helix	311-312	2
α-helix	316-318	3
α-helix	336-338	3

Chain B: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-31	19
α-helix	40-42	3
β-strand	43-52	10	5
β-strand	55-62	8	5
β-strand	68-75	8	5
α-helix	76-81	6
α-helix	85-95	11
β-strand	103	1	6
α-helix	104-105	2
β-strand	106-111	6	5
β-strand	115-120	6	5
β-strand	127	1	6
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	7
α-helix	169-171	3
β-strand	172-174	3	6
β-strand	180-182	3	6
β-strand	189-190	2	7
β-strand	195	1	8
β-strand	200	1	9
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	8
α-helix	218-233	16
α-helix	243-252	10
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
α-helix	316-318	3
α-helix	336-338	3

Chain C: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
α-helix	40-42	3
β-strand	43-52	10	10
β-strand	55-62	8	10
β-strand	68-75	8	10
α-helix	76-81	6
α-helix	85-95	11
β-strand	103	1	11
α-helix	104-105	2
β-strand	106-111	6	10
β-strand	115-120	6	10
β-strand	127	1	11
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	12
α-helix	169-171	3
β-strand	172-174	3	11
β-strand	180-182	3	11
β-strand	189-190	2	12
β-strand	195	1	13
β-strand	200	1	14
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	13
α-helix	218-233	16
α-helix	243-252	10
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
α-helix	316-318	3
α-helix	336-338	3
α-helix	341-342	2

Chain D: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
α-helix	40-42	3
β-strand	43-52	10	15
β-strand	55-62	8	15
β-strand	68-75	8	15
α-helix	76-81	6
α-helix	85-95	11
β-strand	103	1	16
α-helix	104-105	2
β-strand	106-111	6	15
β-strand	115-120	6	15
β-strand	127	1	16
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	17
α-helix	169-171	3
β-strand	172-174	3	16
β-strand	180-182	3	16
β-strand	189-190	2	17
β-strand	195	1	18
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	18
α-helix	218-233	16
α-helix	243-252	10
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
α-helix	316-318	3
α-helix	336-338	3

Chain E: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	17-31	15
α-helix	40-42	3
β-strand	43-52	10	19
β-strand	55-62	8	19
β-strand	68-75	8	19
α-helix	76-81	6
α-helix	85-95	11
β-strand	103	1	20
α-helix	104-105	2
β-strand	106-111	6	19
β-strand	115-120	6	19
β-strand	127	1	20
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	21
α-helix	169-171	3
β-strand	172-174	3	20
β-strand	180-182	3	20
β-strand	189-190	2	21
β-strand	195	1	22
β-strand	200	1	23
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	22
α-helix	218-233	16
α-helix	243-252	10
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
α-helix	316-318	3
α-helix	336-338	3

Chain F: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-31	22
α-helix	40-42	3
β-strand	43-52	10	24
β-strand	55-62	8	24
β-strand	68-75	8	24
α-helix	76-81	6
α-helix	85-95	11
β-strand	103	1	25
α-helix	104-105	2
β-strand	106-111	6	24
β-strand	115-120	6	24
β-strand	127	1	25
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	26
α-helix	169-171	3
β-strand	172-174	3	25
β-strand	180-182	3	25
β-strand	189-190	2	26
β-strand	195	1	27
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	27
α-helix	218-233	16
α-helix	243-252	10
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
α-helix	316-318	3
α-helix	336-338	3
α-helix	341-342	2

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7

Chains H and K: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	18-21	4
β-strand	22	1	9

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-dependent protein kinase catalytic subunit alpha	A, B, C, D, E, F	protein	350	Bos taurus	P00517 (AlphaFold model)
cAMP-dependent protein kinase inhibitor peptide	G, H, I, J, K, L	protein	20		Q3SX13 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>3E8C_1 cAMP-dependent protein kinase catalytic subunit alpha (chains A, B, C, D, E, F)
GNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLV
KHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVM
EYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYI
QVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFA
DQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATT
DWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>3E8C_2 cAMP-dependent protein kinase inhibitor peptide (chains G, H, I, J, K, L)
TTYADFIASGRTGRRNAIHD

Ligands and cofactors

ID	Name	Formula	Copies
G96	4-[2-(4-amino-1,2,5-oxadiazol-3-yl)-6-{[(2R)-2-amino-3-phenylpropyl]oxy}-1-ethy…	C24 H27 N7 O3	6

Primary citation

Aminofurazans as potent inhibitors of AKT kinase. Rouse, M.B., Seefeld, M.A., Leber, J.D. et al. Bioorg Med Chem Lett (2009) 19:1508-1511. DOI 10.1016/j.bmcl.2009.01.002 · 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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