SAXSdb — 4nm7

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1. Protein Identity and Related Structures Protein Identity & Related Structures

GSK3B protein

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 13–383	Fragment：Residues 13-383	Axin-1 × 1 （O15169） Phosphorylated Wnt receptor LRP6 e-motif × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 3 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4NM7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NM5 Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif Deposited 2013-11-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 13–383（371 aa） Fragment：Residues 13-383	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 4 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.232
4NM5 Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif Deposited 2013-11-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 13–383（371 aa） Fragment：Residues 13-383	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 8 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.232

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6FI27_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–371； UniProt 13–383

Axin-1

Homo sapiens

UniProt O15169

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 383–402	Fragment：Residues 383-402	GSK3B protein × 1 （Q6FI27） Phosphorylated Wnt receptor LRP6 e-motif × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 3 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4NM7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DK8 CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN Deposited 1999-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 111–257（147 aa） Fragment：RGS-HOMOLOGOUS DOMAIN	Not recorded	SO4 SULFATE ION × 12 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.25；277 K；sodium acetate, ammonium sulfate, glycerol, dithiothreitol, pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.57 Å R-free 0.198
1EMU STRUCTURE OF THE AXIN RGS-HOMOLOGOUS DOMAIN IN COMPLEX WITH A SAMP REPEAT FROM APC Deposited 2000-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 117–248（132 aa） Fragment：RGS-HOMOLOGOUS DOMAIN	Not recorded	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；MES, PEG 400, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.221
1O9U GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH AXIN PEPTIDE Deposited 2002-12-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 383–400（18 aa） Fragment：RESIDUES 383-400	Not recorded	ADZ 9-METHYL-9H-PURIN-6-AMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTAL WERE GROWN BY THE HANGING DROP METHOD. 1UL OF PROTEIN SOLUTION (6MG/ML GSK3B AND 0.37MG/ML AXIN PEPTIDE) IN 25MM HEPES-NAOH, 250MM NACL, 1MM DTT, PH 7.0) WAS MIXED WITH 1UL PRECIPITANT (18% PEG4000, 150MM MGCL2, 100MM TRIS- HCL, PH 7.5)	Resolution 2.40 Å R-free 0.260
3ZDI Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Inhibitor 7d Deposited 2012-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–400（18 aa） Fragment：RESIDUES 383-400	Not recorded	PO4 PHOSPHATE ION × 1 UGJ 3,6-Diamino-4-(2-chlorophenyl)thieno[2,3-b]pyridine-2,5-dicarbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES), PH 6.5, 12% (W/V) PEG 20000	Resolution 2.65 Å R-free 0.242
4B7T Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Leucettine L4 Deposited 2012-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–400（18 aa） Fragment：RESIDUES 383-400	Not recorded	CWT (5Z)-5-(1,3-benzodioxol-5-ylmethylidene)-3-methyl-2-(propan-2-ylamino)imidazol-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M TRIS-HCL, PH 8.0, 0.15 M MGCL2, 15% (W/V) PEG 4000	Resolution 2.77 Å R-free 0.235
4NM0 Crystal structure of peptide inhibitor-free GSK-3/Axin complex Deposited 2013-11-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	GOL GLYCEROL × 5 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 20mM MgCl2, 400uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.50 Å R-free 0.239
4NM3 Crystal structure of GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide Deposited 2013-11-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	GOL GLYCEROL × 4 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.10 Å R-free 0.242
4NM5 Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif Deposited 2013-11-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 4 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.232
4NM5 Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif Deposited 2013-11-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 8 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.232
4NU1 Crystal structure of a transition state mimic of the GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide Deposited 2013-12-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	GOL GLYCEROL × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris pH7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.50 Å R-free 0.245
5WZZ The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation Deposited 2017-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 375–394（20 aa） Fragment：UNP residues 375-394	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl	Resolution 2.10 Å R-free 0.208
5WZZ The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation Deposited 2017-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 375–394（20 aa） Fragment：UNP residues 375-394	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl	Resolution 2.10 Å R-free 0.208
5WZZ The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation Deposited 2017-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 375–394（20 aa） Fragment：UNP residues 375-394	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl	Resolution 2.10 Å R-free 0.208
5WZZ The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation Deposited 2017-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 375–394（20 aa） Fragment：UNP residues 375-394	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl	Resolution 2.10 Å R-free 0.208
6JCK Complex structure of Axin-DIX and Dvl2-DIX Deposited 2019-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 745–826（82 aa）	Mutation：Y760D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；25% (w/v) PEG1500, 0.1 M Malonate-Imidazole-Borate buffer pH 7.0	Resolution 3.09 Å R-free 0.290
7Y1P CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na Deposited 2022-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 74–220（147 aa） Fragment：RGS-homologous domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；2.4 M sodium malonate pH 7.0	Resolution 2.60 Å R-free 0.228
7Y1P CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na Deposited 2022-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 74–220（147 aa） Fragment：RGS-homologous domain	Not recorded	I5L (2~{Z},4~{Z})-2-methyl-5-(8-oxidanyldibenzofuran-4-yl)penta-2,4-dienal × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；2.4 M sodium malonate pH 7.0	Resolution 2.60 Å R-free 0.228
7Y1P CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na Deposited 2022-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 74–220（147 aa） Fragment：RGS-homologous domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；2.4 M sodium malonate pH 7.0	Resolution 2.60 Å R-free 0.228
7Y1P CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na Deposited 2022-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 74–220（147 aa） Fragment：RGS-homologous domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；2.4 M sodium malonate pH 7.0	Resolution 2.60 Å R-free 0.228
8RU3 Crystal structure of beta-catenin in complex with alpha-helical peptide inhibitor Deposited 2024-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 468–479（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；300 K；Crystals grown in 100 mM NaKPO4, 2M NaCl.	Resolution 2.00 Å R-free 0.232
8RU4 Crystal structure of Human Catenin Beta-1 in complex with stitched peptide inhibitor Deposited 2024-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 469–479（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GLC alpha-D-glucopyranose × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；100 mM TRIS pH 8.75, 2%(w/v) PEG-6000, cryoprotected in 30% (w/v) Glucose.	Resolution 2.13 Å R-free 0.240
8VMG Crystal structure of GSK-3 26-383 bound to Axin 383-435 Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 383–435（53 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 20 NO3 NITRATE ION × 8 GOL GLYCEROL × 4 SO4 SULFATE ION × 7 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM MES, pH 5.5, 1.9 M ammonium sulfate, 200 mM sodium chloride, cryoprotectant: 25% ethylene glycol	Resolution 2.45 Å R-free 0.230
8VMG Crystal structure of GSK-3 26-383 bound to Axin 383-435 Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 383–435（53 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 19 SO4 SULFATE ION × 2 CL CHLORIDE ION × 8 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM MES, pH 5.5, 1.9 M ammonium sulfate, 200 mM sodium chloride, cryoprotectant: 25% ethylene glycol	Resolution 2.45 Å R-free 0.230

15 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AXIN1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–24； UniProt 383–402

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4nm7
Deposition date deposition_date	2013-11-14
Structure title title	Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 e-motif
Keywords keywords	;Wnt, LRP6, Auto-inhibited, GSK-3, primed substrate, Kinase, Axin, phosphorylated Wnt receptor LRP6 e-motif, TRANSFERASE-PEPTIDE complex ;; TRANSFERASE/PEPTIDE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.93 Å
Radius of gyration Rg (electron density) rg_electron	21.82 Å
Forward intensity I(0) i0	30954400.00
Molecular weight molecular_weight	43096.0 kDa
Excluded volume excluded_volume	54138 Å³
Envelope volume envelope_volume	64626 Å³
Hydration-shell volume shell_volume	24648 Å³
Envelope diameter envelope_diameter	77.3 Å
Shell Rg shell_rg	29.05 Å
Envelope Rg envelope_rg	22.25 Å
Shape Rg shape_rg	21.84 Å
Total Rg total_rg	22.70 Å
Total atoms total_atoms	3029
Residues n_residues	379
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	76.2 Å
Rg (real space) rg_real	22.88 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	3.0950e+07
I(0) uncertainty (real space) i0_real_error	4.1090e+05
Rg (reciprocal space) rg_reciprocal	22.89 Å
I(0) (reciprocal space) i0_reciprocal	30950000.0000
Solution quality estimate total_estimate	0.8847
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.311
Kurtosis Kurtosis kurtosis	-0.286
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9007000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	GSK3B protein
Molecular weight formula_weight	42857.2 kDa
EC 编号 ec_number	2.7.11.26
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3198

SCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Axin-1
Molecular weight formula_weight	2738.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GGILVEPQKFAEELIHRLEAVQRT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Phosphorylated Wnt receptor LRP6 e-motif
Molecular weight formula_weight	1006.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MPPPPSPCT

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	106

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4nm7a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d4nm7a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	4nm7A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	4nm7A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	82.002 Å
Unit-cell length b length_b	82.002 Å
Unit-cell length c length_c	280.345 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	39.350 Å
R factor r_factor	0.1850
R_work r_work	0.1830
R_free r_free	0.2340

fit	/app/data/saxs_computation/nm/4nm7/4nm7.fit
pddf	/app/data/pr_computation/nm/4nm7/4nm7.pr.out
profile	/app/data/saxs_computation/nm/4nm7/4nm7.dat

Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 e-motif

1. Protein Identity and Related Structures Protein Identity & Related Structures

GSK3B protein

State in the Current Structure

Other States of the Same Protein in the Database

Axin-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)