8FE2: J-PKAc chimera

Structure of J-PKAc chimera complexed with Aplithianine A. Determined by X-ray diffraction at 2.34 Å resolution. Released 18 Oct 2023.

Method: X-ray diffraction
Resolution: 2.34 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,057
Mol. weight: 100.24 kDa
Ligands: XTI
Released: 18 Oct 2023

Explore 8FE2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FE2 contains 51 α-helices and 30 β-strands across 4 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: 26 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	16-28	13
α-helix	32-34	3
α-helix	40-55	16
α-helix	57-63	7
α-helix	65-86	22
α-helix	95-97	3
β-strand	98-106	9	1
β-strand	110-117	8	1
β-strand	123-130	8	1
α-helix	131-136	6
α-helix	140-150	11
β-strand	158	1	2
α-helix	159-160	2
β-strand	161-166	6	1
β-strand	170-176	7	1
β-strand	182	1	2
α-helix	183-190	8
α-helix	195-214	20
β-strand	217-218	2	3
α-helix	224-226	3
β-strand	227-229	3	2
β-strand	235-237	3	2
β-strand	244-245	2	3
β-strand	250	1	4
β-strand	254-255	2	5
α-helix	257-259	3
α-helix	262-265	4
β-strand	270	1	4
α-helix	273-288	16
α-helix	298-306	9
α-helix	311-313	3
α-helix	318-327	10
α-helix	332-334	3
α-helix	343-347	5
α-helix	350-352	3
α-helix	357-362	6
α-helix	366-367	2
α-helix	379-381	3
α-helix	400-402	3

Chain B: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	16-29	14
α-helix	40-55	16
α-helix	57-63	7
α-helix	65-86	22
α-helix	95-97	3
β-strand	98-105	8	6
β-strand	110-117	8	6
β-strand	123-130	8	6
α-helix	131-136	6
α-helix	140-150	11
β-strand	158	1	7
β-strand	161-166	6	6
β-strand	170-176	7	6
β-strand	182	1	7
α-helix	183-190	8
α-helix	195-214	20
β-strand	217-218	2	8
α-helix	224-226	3
β-strand	227-229	3	7
β-strand	235-237	3	7
β-strand	244-245	2	8
β-strand	250	1	9
β-strand	255	1	10
α-helix	257-259	3
α-helix	262-265	4
β-strand	270	1	9
α-helix	273-288	16
α-helix	298-307	10
α-helix	318-327	10
α-helix	332-334	3
α-helix	344-347	4
α-helix	350-352	3
α-helix	357-361	5
α-helix	366-367	2

Chain I: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	18-21	4
β-strand	22-23	2	5

Chain J: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	18-21	4
β-strand	22	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DnaJ homolog subfamily B member 1, cAMP-dependent protein kinase catalytic subunit alpha	A, B	protein	405	Homo sapiens	P17612 (AlphaFold model), P25685 (AlphaFold model)
cAMP-dependent protein kinase inhibitor alpha	I, J	protein	20	Homo sapiens	P61925 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8FE2_1 DnaJ homolog subfamily B member 1, cAMP-dependent protein kinase catalytic subunit alpha (chains A, B)
GKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKR
EIFDRYGEEVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKET
GNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPG
GEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDF
GFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQ
IYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAI
YQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Sequence of entity 2 (I, J), FASTA

>8FE2_2 cAMP-dependent protein kinase inhibitor alpha (chains I, J)
TTYADFIASGRTGRRNAIHD

Ligands and cofactors

ID	Name	Formula	Copies
XTI	6-[(6M)-6-(1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-9H-purine	C13 H13 N7 S	2

Primary citation

Discovery and Synthesis of a Naturally Derived Protein Kinase Inhibitor that Selectively Inhibits Distinct Classes of Serine/Threonine Kinases. Du, L., Wilson, B.A.P., Li, N. et al. J Nat Prod (2023) 86:2283-2293. DOI 10.1021/acs.jnatprod.3c00394 · PubMed

Other PDB entries of the same protein (UniProt P17612 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WB8 1.55 Å, Crystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit),…
3OVV 1.58 Å, Human cAMP-dependent protein kinase in complex with an inhibitor
3POO 1.6 Å, human cAMP-dependent protein kinase in complex with an inhibitor
4WB5 1.64 Å, Crystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit)
6QJ7 1.69 Å, Difluorophenyl diacylhydrazides: Potent inhibitors of Serum- and…
3AMA 1.75 Å, Protein kinase A sixfold mutant model of Aurora B with inhibitor JNJ-7706621
4UJ1 1.77 Å, Protein Kinase A in complex with an Inhibitor
5IZJ 1.85 Å, Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1411
4UJ9 1.87 Å, Protein Kinase A in complex with an Inhibitor
3OWP 1.88 Å, Human cAMP-dependent protein kinase in complex with an inhibitor
6FRX 1.88 Å, PKA variant as Aurora B mimic in complex with a dianilinopyrimidine inhibitor
5BX6 1.89 Å, PKA in complex with a halogenated phthalazinone fragment compound.

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