5OY4: Glycogen synthase kinase-3 beta

GSK3beta complex with N-(6-(3,4-dihydroxyphenyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)acetamide. Determined by X-ray diffraction at 3.2 Å resolution. Released 1 Nov 2017.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,988
Mol. weight: 152.98 kDa
Ligands: B4K
Released: 1 Nov 2017

Explore 5OY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OY4 contains 51 α-helices and 26 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: 22 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	38-44	7	1
β-strand	52-64	13	1
β-strand	69-75	7	1
β-strand	81-90	10	1
α-helix	96-103	8
β-strand	109	1	2
β-strand	112-119	8	1
β-strand	125-133	9	1
β-strand	137-138	2	2
α-helix	139-148	10
α-helix	152-154	3
α-helix	155-173	19
β-strand	177-178	2	3
α-helix	184-186	3
β-strand	187-189	3	2
β-strand	196-198	3	2
β-strand	205-206	2	3
α-helix	220-222	3
α-helix	225-228	4
α-helix	237-252	16
α-helix	262-273	12
α-helix	276-277	2
α-helix	278-284	7
α-helix	297-300	4
α-helix	301-304	4
α-helix	311-318	8
α-helix	325-327	3
α-helix	329-330	2
α-helix	331-335	5
α-helix	338-344	7
α-helix	354-356	3
α-helix	371-373	3
α-helix	374-377	4
α-helix	380-382	3

Chain B: 25 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	35-37	3
β-strand	38-44	7	4
β-strand	52-65	14	4
β-strand	68-75	8	4
β-strand	81-90	10	4
α-helix	96-103	8
β-strand	109	1	5
β-strand	112-119	8	4
β-strand	125-133	9	4
β-strand	137-138	2	5
α-helix	139-148	10
α-helix	152-154	3
α-helix	155-173	19
β-strand	177-178	2	6
α-helix	184-186	3
β-strand	187-189	3	5
β-strand	196-198	3	5
β-strand	205-206	2	6
α-helix	220-222	3
α-helix	225-228	4
α-helix	237-252	16
α-helix	262-273	12
α-helix	276-277	2
α-helix	278-284	7
α-helix	297-300	4
α-helix	301-304	4
α-helix	311-318	8
α-helix	325-327	3
α-helix	329-330	2
α-helix	331-335	5
α-helix	338-344	7
β-strand	349	1	7
α-helix	354	1
β-strand	355	1	7
α-helix	356-358	3
α-helix	364-367	4
α-helix	371-373	3
α-helix	374-377	4
α-helix	380-382	3

Chain X: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	200-209	10
α-helix	212-222	11

Chain Y: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	200-209	10
α-helix	212-221	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycogen synthase kinase-3 beta	A, B	protein	420	Homo sapiens	P49841 (AlphaFold model)
Proto-oncogene FRAT1	X, Y	protein	279	Homo sapiens	Q92837 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5OY4_1 Glycogen synthase kinase-3 beta (chains A, B)
MSGRPRTTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTK
VIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSG
EKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHR
DIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDV
WSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHP
WTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALF
NFTTQELSSNPPLATILIPPHARIQAAASTPTNATAASDANTGDRGQTNNAASASASNST

Sequence of entity 2 (X, Y), FASTA

>5OY4_2 Proto-oncogene FRAT1 (chains X, Y)
MPCRREEEEEAGEEAEGEEEEEDSFLLLQQSVALGSSGEVDRLVAQIGETLQLDAAQHSP
ASPCGPPGAPLRAPGPLAAAVPADKARSPAVPLLLPPALAETVGPAPPGVLRCALGDRGR
VRGRAAPYCVAELATGPSALSPLPPQADLDGPPGAGKQGIPQPLSGPCRRGWLRGAAASR
RLQQRRGSQPETRTGDDDPHRLLQQLVLSGNLIKEAVRRLHSRRLQLRAKLPQRPLLGPL
SAPVHEPPSPRSPRAACSDPGASGRAQLRTGDGVLVPGS

Ligands and cofactors

ID	Name	Formula	Copies
B4K	~{N}-[6-[3,4-bis(oxidanyl)phenyl]-1~{H}-pyrazolo[3,4-b]pyridin-3-yl]ethanamide	C14 H12 N4 O3	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

From PIM1 to PI3K delta via GSK3 beta : Target Hopping through the Kinome. Henley, Z.A., Bax, B.D., Inglesby, L.M. et al. ACS Med Chem Lett (2017) 8:1093-1098. DOI 10.1021/acsmedchemlett.7b00296 · PubMed

Other PDB entries of the same protein (UniProt P49841 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X2V 1.39 Å, GSK3beta complexed with BiS-3
1O6L 1.6 Å, Crystal structure of an activated Akt/protein kinase B (PKB-PIF chimera) ternary complex…
9X2Q 1.68 Å, GSK3beta complexed with BiS-1
1O6K 1.7 Å, Structure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP
9X2X 1.79 Å, GSK3beta complexed with BiS-5
1J1B 1.8 Å, Binary complex structure of human tau protein kinase I with AMPPNP
2JDO 1.8 Å, Structure of pkb-beta (AKT2) complexed with isoquinoline-5-sulfonic acid…
7SXJ 1.85 Å, BIO-2895 (BRD0705) bound GSK3beta-axin complex
3QKL 1.9 Å, Spirochromane Akt Inhibitors
9X2W 1.92 Å, GSK3beta complexed with BiS-4
2X39 1.93 Å, Structure of 4-Amino-N-(4-chlorobenzyl)-1-(7H-pyrrolo(2,3-d)pyrimidin-…
1Q5K 1.94 Å, crystal structure of Glycogen synthase kinase 3 in complexed with inhibitor

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