6AE3

Crystal structure of GSK3beta complexed with Morin

PDB DOI: https://doi.org/10.2210/pdb6AE3/pdb

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2018-08-03 Released: 2018-09-19
Deposition Author(s): Kim, K.L., Cha, J.S., Kim, J.S., Ahn, J.S., Ha, N.C., Cho, H.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 ?
R-Value Free: 0.226
R-Value Work: 0.191
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of GSK3 beta in complex with the flavonoid, morin

Kim, K., Cha, J.S., Kim, J.S., Ahn, J., Ha, N.C., Cho, H.S.

(2018) Biochem Biophys Res Commun 504: 519-524

PubMed: 30197003 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2018.08.182
Primary Citation of Related Structures:
6AE3

PubMed Abstract:
GSK3β is a key kinase that plays a role in cellular signaling pathways. In Alzheimer's disease (AD), GSK3β has been implicated in hyperphosphorylation of tau proteins in the neuron, which is a hallmark of AD. Morin, a flavonoid that is abundant in nature, was found as an inhibitor of GSK3β that can reduce tau pathology in?vivo and in?vitro. In this study, we determined the crystal structure of GSK3β in complex with morin. The structure revealed that morin inhibits GSK3β by binding to the ATP binding pocket. Our findings augment the potential of morin as a functional food to help prevent AD, as well as to provide structural information to develop new therapeutics based on the morin skeleton.

Organizational Affiliation

Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA.

Macromolecule Content

Total Structure Weight: 188.36 kDa
Atom Count: 10,953
Modelled Residue Count: 1,357
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B, C, D	420	Mus musculus	Mutation(s): 0 Gene Names: Gsk3b EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q9WV60 (Mus musculus) Explore Q9WV60 Go to UniProtKB: Q9WV60
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WV60
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRI (Subject of Investigation/LOI) Query on MRI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one C₁₅ H₁₀ O₇ YXOLAZRVSSWPPT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D]	F [auth A], H [auth B], I [auth C], J [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A, B, C, D	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 ?
R-Value Free: 0.226
R-Value Work: 0.191
R-Value Observed: 0.192
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 67.588	α = 90
b = 134.36	β = 103.8
c = 100.393	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-09-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-19
Type: Initial release
Version 1.1: 2018-09-26
Changes: Data collection, Database references
Version 1.2: 2018-10-03
Changes: Data collection, Database references
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary