6BYR: PDB entry 6BYR

Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha. Determined by X-ray diffraction at 3.66 Å resolution. Released 3 Apr 2019.

Method: X-ray diffraction
Resolution: 3.66 Å
Organisms: Homo sapiens, Bos taurus
Chains: 4
Atoms: 11,358
Mol. weight: 181.93 kDa
Ligands: ATP, MG
Released: 3 Apr 2019

Explore 6BYR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BYR contains 70 α-helices and 70 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: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	16-23	8
α-helix	41-43	3
α-helix	47-50	4
α-helix	61-86	26
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
α-helix	177	1
β-strand	182	1	2
α-helix	183-190	8
α-helix	195-213	19
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	249-250	2	4
β-strand	254-255	2	5
α-helix	257-259	3
α-helix	262-265	4
β-strand	270-271	2	4
α-helix	273-288	16
α-helix	298-307	10
α-helix	318-327	10
α-helix	344-347	4
α-helix	350-352	3
α-helix	357-362	6

Chain B: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	94-97	4
β-strand	98-99	2	5
α-helix	100-102	3
α-helix	105-109	5
α-helix	120-129	10
α-helix	141-148	8
β-strand	152-156	5	6
β-strand	161-163	3	7
β-strand	168	1	8
α-helix	169	1
β-strand	171-177	7	6
β-strand	180-183	4	7
β-strand	188-192	5	7
β-strand	197-198	2	6
α-helix	200-203	4
β-strand	208	1	8
β-strand	212-214	3	7
β-strand	219-225	7	6
α-helix	226-250	25
α-helix	253-256	4
α-helix	259-266	8
β-strand	270-274	5	9
β-strand	279-281	3	9
β-strand	286-287	2	10
β-strand	289	1	11
β-strand	291-302	12	9
β-strand	311-314	4	9
β-strand	321-322	2	9
α-helix	324-327	4
β-strand	331-332	2	10
β-strand	336-347	12	9
β-strand	349	1	11
α-helix	350-356	7
α-helix	360-364	5
α-helix	368-378	11

Chain C: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	24-30	7
α-helix	43-46	4
α-helix	47-50	4
α-helix	57-86	30
α-helix	95-97	3
β-strand	98-105	8	12
β-strand	111-117	7	12
β-strand	123-130	8	12
α-helix	131-136	6
α-helix	140-150	11
β-strand	158	1	13
α-helix	159-160	2
β-strand	161-166	6	12
β-strand	170-176	7	12
α-helix	177-178	2
β-strand	181-182	2	13
α-helix	183-190	8
α-helix	195-214	20
β-strand	217-218	2	14
α-helix	224-226	3
β-strand	227-229	3	13
β-strand	235-237	3	13
β-strand	244-245	2	14
β-strand	250	1	15
β-strand	254-255	2	16
α-helix	257-259	3
α-helix	262-265	4
β-strand	270	1	15
α-helix	273-288	16
α-helix	298-307	10
α-helix	320-327	8
α-helix	344-347	4
α-helix	350-352	3
α-helix	357-361	5
α-helix	366-367	2
α-helix	383-384	2

Chain D: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	94-97	4
β-strand	98-99	2	16
α-helix	105-109	5
α-helix	120-129	10
α-helix	141-150	10
β-strand	152-156	5	17
β-strand	161-163	3	18
β-strand	165	1	19
β-strand	167	1	19
β-strand	168	1	20
α-helix	169	1
β-strand	171-177	7	17
β-strand	180-184	5	18
β-strand	187-192	6	18
β-strand	197-198	2	17
α-helix	200-203	4
β-strand	208	1	20
β-strand	212-214	3	18
β-strand	219-225	7	17
α-helix	226-249	24
α-helix	253-256	4
α-helix	259-268	10
β-strand	270-274	5	21
β-strand	279	1	21
β-strand	286-287	2	22
β-strand	289-302	14	21
β-strand	311-316	6	21
β-strand	321-322	2	21
α-helix	324-327	4
β-strand	331-332	2	22
β-strand	336-349	14	21
α-helix	350-357	8
α-helix	360-364	5
α-helix	368-378	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera	A, C	protein	405	Homo sapiens	P17612 (AlphaFold model), P25685 (AlphaFold model)
cAMP-dependent protein kinase type I-alpha regulatory subunit	B, D	protein	379	Bos taurus	P00514 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6BYR_1 DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha chimera (chains A, C)
GKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKR
EIFDRYGEEVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKET
GNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPG
GEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDF
GFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQ
IYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAI
YQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Sequence of entity 2 (B, D), FASTA

>6BYR_2 cAMP-dependent protein kinase type I-alpha regulatory subunit (chains B, D)
ASGTTASEEERSLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFEKLEKEEA
KQIQNLQKAGSRADSREDEISPPPPNPVVKGRRRRGAISAEVYTEEDAASYVRKVIPKDY
KTMAALAKAIEKNVLFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEM
DVYVNNEWATSVGEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRK
RKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQKIVVQGEPGDEFFIILEGSAAV
LQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVKLDRPRFERVLGPC
SDILKRNIQQYNSFVSLSV

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	4

Primary citation

Structures of the PKA RI alpha Holoenzyme with the FLHCC Driver J-PKAc alpha or Wild-Type PKAc alpha. Cao, B., Lu, T.W., Martinez Fiesco, J.A. et al. Structure (2019) 27:816. DOI 10.1016/j.str.2019.03.001 · 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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