3E8E: Kinase domain of PKA

Crystal structures of the kinase domain of PKA in complex with ATP-competitive inhibitors. Determined by X-ray diffraction at 2.0 Å resolution. Released 18 Nov 2008.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Bos taurus
Chains: 12
Atoms: 18,474
Mol. weight: 260.86 kDa
Ligands: G98
Released: 18 Nov 2008

Explore 3E8E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3E8E contains 121 α-helices and 79 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: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
α-helix	40-42	3
β-strand	43-51	9	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	243-252	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

Chain B: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-31	19
α-helix	40-42	3
β-strand	43-51	9	5
β-strand	55-62	8	5
β-strand	68-75	8	5
α-helix	76-81	6
α-helix	85-97	13
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
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	341-342	2

Chains C, G and J: 2 helices, 0 β-strands

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

Chain E: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-31	21
α-helix	40-42	3
β-strand	43-51	9	9
β-strand	55-62	8	9
β-strand	68-75	8	9
α-helix	76-81	6
α-helix	85-97	13
β-strand	103	1	10
α-helix	104-105	2
β-strand	106-111	6	9
β-strand	115-120	6	9
β-strand	127	1	10
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	11
α-helix	169-171	3
β-strand	172-174	3	10
β-strand	180-182	3	10
β-strand	189-190	2	11
β-strand	195	1	12
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	12
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	316-318	3
α-helix	336-338	3

Chains F and N: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7

Chain I: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	11-31	21
α-helix	40-42	3
β-strand	43-52	10	13
β-strand	55-62	8	13
β-strand	68-75	8	13
α-helix	76-81	6
α-helix	85-97	13
β-strand	103	1	14
α-helix	104-105	2
β-strand	106-111	6	13
β-strand	115-121	7	13
β-strand	127	1	14
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	15
α-helix	169-171	3
β-strand	172-174	3	14
β-strand	180-182	3	14
β-strand	189-190	2	15
β-strand	195	1	16
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	16
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

Chain L: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	40-42	3
β-strand	43-51	9	17
β-strand	55-62	8	17
β-strand	68-75	8	17
α-helix	76-81	6
α-helix	85-97	13
β-strand	103	1	18
α-helix	104-105	2
β-strand	106-111	6	17
β-strand	115-121	7	17
β-strand	127	1	18
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	19
α-helix	169-171	3
β-strand	172-174	3	18
β-strand	180-182	3	18
β-strand	189-190	2	19
β-strand	195	1	20
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	20
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

Chain P: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	10-31	22
β-strand	36	1	21
α-helix	40-42	3
β-strand	43-51	9	21
β-strand	55-62	8	21
β-strand	68-75	8	21
α-helix	76-81	6
α-helix	85-97	13
β-strand	103	1	22
α-helix	104-105	2
β-strand	106-111	6	21
β-strand	115-120	6	21
β-strand	127	1	22
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	23
α-helix	169-171	3
β-strand	172-174	3	22
β-strand	180-182	3	22
β-strand	189-190	2	23
β-strand	195	1	24
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	24
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

1 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, E, I, L, P	protein	350	Bos taurus	P00517 (AlphaFold model)
PKI inhibitor peptide	C, F, G, J, N, Q	protein	20		Q3SX13 (AlphaFold model)

Sequence of entity 1 (A, B, E, I, L, P), FASTA

>3E8E_1 cAMP-dependent protein kinase catalytic subunit alpha (chains A, B, E, I, L, P)
GNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLV
KHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVM
EYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYI
QVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFA
DQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATT
DWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Sequence of entity 2 (C, F, G, J, N, Q), FASTA

>3E8E_2 PKI inhibitor peptide (chains C, F, G, J, N, Q)
TTYADFIASGRTGRRNAIHD

Ligands and cofactors

ID	Name	Formula	Copies
G98	4-[2-(4-amino-2,5-dihydro-1,2,5-oxadiazol-3-yl)-6-{[(1S)-3-amino-1-phenylpropyl…	C24 H29 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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