4NM3: GSK-3/Axin complex

Crystal structure of GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 26 Mar 2014.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,297
Mol. weight: 48.03 kDa
Ligands: MG, DTT, ADP
Released: 26 Mar 2014

Explore 4NM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NM3 contains 22 α-helices and 13 β-strands across 2 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: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	1
β-strand	37-44	8	1
β-strand	52-63	12	1
β-strand	69-75	7	1
β-strand	81-88	8	1
α-helix	97-101	5
β-strand	109	1	2
β-strand	112-118	7	1
β-strand	127-133	7	1
β-strand	137-138	2	2
α-helix	139-148	10
α-helix	155-173	19
β-strand	177-178	2	3
α-helix	184-186	3
β-strand	187-190	4	2
β-strand	195-198	4	2
β-strand	205-206	2	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	286-288	3
α-helix	296-300	5
α-helix	301-304	4
α-helix	311-320	10
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	380-383	4

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	385-400	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycogen synthase kinase-3 beta	A	protein	389	Homo sapiens	P49841 (AlphaFold model)
Axin-1	B	protein	24	Homo sapiens	O15169 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4NM3_1 Glycogen synthase kinase-3 beta (chains A)
MSGRPRTTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTK
VIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSG
EKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHR
DIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDV
WSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHP
WTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALF
NFTTQELSSNPPLATILIPPHARHHHHHH

Sequence of entity 2 (B), FASTA

>4NM3_2 Axin-1 (chains B)
GGILVEPQKFAEELIHRLEAVQRT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6. Stamos, J.L., Chu, M.L., Enos, M.D. et al. Elife (2014) 3:e01998-e01998. 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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