8VMG

Crystal structure of GSK-3 26-383 bound to Axin 383-435

PDB DOI: https://doi.org/10.2210/pdb8VMG/pdb

Classification: TRANSFERASE/SIGNALING PROTEIN
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-13 Released: 2024-08-28
Deposition Author(s): Enos, M.D., Gavagan, M., Jameson, N., Zalatan, J.G., Weis, W.I.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.230
R-Value Work: 0.195
R-Value Observed: 0.195

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural and functional effects of phosphopriming and scaffolding in the kinase GSK3beta

Enos, M.D., Gavagan, M., Jameson, N., Zalatan, J.G., Weis, W.I.

(2024) Sci Signal

DOI: https://doi.org/10.1126/scisignal.ado0881

Macromolecule Content

Total Structure Weight: 101.72 kDa
Atom Count: 6,672
Modelled Residue Count: 778
Deposited Residue Count: 848
Unique protein chains: 2

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	364	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Axin-1	C, D	60	Homo sapiens	Mutation(s): 0 Gene Names: AXIN1, AXIN
UniProt & NIH Common Fund Data Resources
Find proteins for O15169 (Homo sapiens) Explore O15169 Go to UniProtKB: O15169
PHAROS: O15169 GTEx: ENSG00000103126
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15169
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain TA [auth B] MOL2 format, chain TA [auth B]	TA [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain TA [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AC [auth C] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NB [auth B] SDF format, chain OB [auth B] MOL2 format, chain AC [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain OB [auth B]	AC [auth C] HA [auth A] IA [auth A] JA [auth A] KA [auth A] AC [auth C], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NB [auth B], OB [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AC [auth C] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NB [auth B] Focus chain OB [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain N [auth A] SDF format, chain R [auth A] SDF format, chain W [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth A]	CA [auth A], N [auth A], R [auth A], W [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain N [auth A] Focus chain R [auth A] Focus chain W [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain F [auth A] SDF format, chain FB [auth B] SDF format, chain G [auth A] SDF format, chain GB [auth B] SDF format, chain H [auth A] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain WB [auth C] SDF format, chain XA [auth B] SDF format, chain XB [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain YB [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZB [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain YB [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth C]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CB [auth B] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CB [auth B], DA [auth A], DB [auth B], EB [auth B], F [auth A], FB [auth B], G [auth A], GB [auth B], H [auth A], HB [auth B], I [auth A], IB [auth B], J [auth A], JB [auth B], KB [auth B], LB [auth B], MB [auth B], O [auth A], Q [auth A], S [auth A], T [auth A], U [auth A], UA [auth B], V [auth A], VA [auth B], WA [auth B], WB [auth C], XA [auth B], XB [auth C], Y [auth A], YA [auth B], YB [auth C], Z [auth A], ZA [auth B], ZB [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain F [auth A] Focus chain FB [auth B] Focus chain G [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain O [auth A] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain X [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain X [auth A]	EA [auth A] FA [auth A] GA [auth A] K [auth A] L [auth A] EA [auth A], FA [auth A], GA [auth A], K [auth A], L [auth A], M [auth A], P [auth A], X [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth A] Focus chain X [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BC [auth C] SDF format, chain CC [auth C] SDF format, chain DC [auth D] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain PB [auth B] SDF format, chain QA [auth A] SDF format, chain QB [auth B] SDF format, chain RA [auth A] SDF format, chain RB [auth B] SDF format, chain SA [auth A] SDF format, chain SB [auth B] SDF format, chain TB [auth B] SDF format, chain UB [auth B] SDF format, chain VB [auth B] MOL2 format, chain BC [auth C] MOL2 format, chain CC [auth C] MOL2 format, chain DC [auth D] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain TB [auth B] MOL2 format, chain UB [auth B] MOL2 format, chain VB [auth B]	BC [auth C] CC [auth C] DC [auth D] OA [auth A] PA [auth A] BC [auth C], CC [auth C], DC [auth D], OA [auth A], PA [auth A], PB [auth B], QA [auth A], QB [auth B], RA [auth A], RB [auth B], SA [auth A], SB [auth B], TB [auth B], UB [auth B], VB [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BC [auth C] Focus chain CC [auth C] Focus chain DC [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain RA [auth A] Focus chain RB [auth B] Focus chain SA [auth A] Focus chain SB [auth B] Focus chain TB [auth B] Focus chain UB [auth B] Focus chain VB [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain NA [auth A] MOL2 format, chain NA [auth A]	NA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain NA [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.230
R-Value Work: 0.195
R-Value Observed: 0.195
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.585	α = 90
b = 195.585	β = 90
c = 152.204	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
XDS	data reduction
pointless	data scaling
Aimless	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM131747
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119156
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM007276