3s2k

Structural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6.

Method: X-RAY DIFFRACTION D_max: 159.3 Å Quality: GOOD

▼

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

Low-density lipoprotein receptor-related protein 6

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	Other combination Heteromer Protein × 3 其他Polymer 4 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 630–1246 Chain B； UniProt 630–1246	Fragment：ectodomain repeats 3, 4 UNP residues 630-1246	Dickkopf-related protein 1 × 1 （O94907） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；10-15% PEG3350, 100 mM Tris-Cl (pH 8.5), 100 mM Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.251

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 3S2K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21KR A Wnt3a/Fzd8-CRD/LRP6-E3E4 complex with FKBP Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 630–1245（616 aa） Chain F 630–1245（616 aa）	Mutation：C715S Mutation：C715S	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.90 Å
21KS A Wnt3a/Fzd8-CRD/LRP6-E3E4-LA complex with FKBP Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 630–1370（741 aa） Chain F 630–1370（741 aa）	Mutation：C840S Mutation：C840S	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.01 Å
21KT Wnt3a signalosome extracellular complex Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain B 630–1245（616 aa） Chain F 630–1245（616 aa）	Mutation：C715S Mutation：C715S	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.33 Å
3S8V Crystal structure of LRP6-Dkk1 complex Deposited 2011-05-31	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 629–1243（615 aa） Fragment：E3E4, residues 629-1243	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；298 K；20mM citric acid, 80mM Bis-tris propane pH 8.8, 19-20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.292
3S8V Crystal structure of LRP6-Dkk1 complex Deposited 2011-05-31	Different construct Different mutation/modification 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 629–1243（615 aa） Fragment：E3E4, residues 629-1243	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；298 K；20mM citric acid, 80mM Bis-tris propane pH 8.8, 19-20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.292
3S8Z Crystal structure of LRP6-E3E4 Deposited 2011-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 629–1243（615 aa） Fragment：E3E4, residues 629-1243	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM ADA pH 6.5, 100mM MgCl2, 12% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.282
3S94 Crystal structure of LRP6-E1E2 Deposited 2011-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–630（611 aa） Fragment：E1E2, residues 20-630	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；80mM sodium citrate pH 5.5, 20-21% PEG3350, 40mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.296
3S94 Crystal structure of LRP6-E1E2 Deposited 2011-05-31	Different construct Different mutation/modification 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 20–630（611 aa） Fragment：E1E2, residues 20-630	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；80mM sodium citrate pH 5.5, 20-21% PEG3350, 40mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.296
3SOB The structure of the first YWTD beta propeller domain of LRP6 in complex with a FAB Deposited 2011-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–335（316 aa） Fragment：UNP residues 20-335	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M NaCl, 0.1 M Tris pH 8, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.212
3SOQ The structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1 peptide Deposited 2011-06-30	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 A 20–326（307 aa） Fragment：UNP residues 20-335	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 1 GOL GLYCEROL × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M potassium thiocyanate and 30% (w/v) PEG MME 2000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.221
3SOV The structure of a beta propeller domain in complex with peptide S Deposited 2011-06-30	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 A 20–326（307 aa） Fragment：UNP residues 20-335	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 FUC alpha-L-fucopyranose × 4 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M potassium thiocyanate and 30% (w/v) PEG MME 2000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.27 Å R-free 0.180
4A0P Crystal structure of LRP6P3E3P4E4 Deposited 2011-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 629–1244（616 aa） Fragment：P3E3P4E4, RESIDUES 629-1244	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 3 CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.211
4DG6 Crystal structure of domains 1 and 2 of LRP6 Deposited 2012-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–635（616 aa） Fragment：UNP residues 20-635	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 5.9；292 K；20% PEG 8000, 20mM ammonium sulfate, pH 5.9, hanging drop, temperature 292K	Resolution 2.90 Å R-free 0.313
5AIR Structural analysis of mouse GSK3beta fused with LRP6 peptide. Deposited 2015-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1565–1575（11 aa） Fragment：;RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420 ; Chain B 1565–1575（11 aa） Fragment：;RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420 ;	Not recorded	MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；200 MM SODIUM MALONATE, 20 % (V/V) PEG 3350, pH 7	Resolution 2.53 Å R-free 0.260
5FWW Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) Deposited 2016-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 630–1246（617 aa） Fragment：PE3PE4, RESIDUES 630-1246	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20 %W/V PEG3350 0.2 M NA/K-PHOSPHATE, pH 7.5	Resolution 3.50 Å R-free 0.355
5GJE Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 Deposited 2016-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–630（611 aa） Fragment：UNP residues 20-630 Chain B 631–1246（616 aa） Fragment：UNP residues 631-1246	Mutation：V1062I	PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2	Resolution 21.00 Å
6H15 Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-B10 Deposited 2018-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 630–1244（615 aa） Chain B 630–1244（615 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CL CHLORIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M sodium citrate, 0.2 M sodium acetate trihydrate pH 5.5, 10 % PEG w/v 4000	Resolution 2.60 Å R-free 0.247
6H16 Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-D07 Deposited 2018-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 630–1244（615 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES pH 5.0, 10 % w/v PEG 6000	Resolution 2.90 Å R-free 0.252
6L6R Crystal structure of LRP6 E1E2-SOST complex Deposited 2019-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–630（610 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MG MAGNESIUM ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；301 K；PEG 8000, magnesium acetate, sodium citrate, HEPES	Resolution 3.80 Å R-free 0.256
6L6R Crystal structure of LRP6 E1E2-SOST complex Deposited 2019-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 21–630（610 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；301 K；PEG 8000, magnesium acetate, sodium citrate, HEPES	Resolution 3.80 Å R-free 0.256
7NAM LRP6_E1 in complex with Lr-EET-3.5 Deposited 2021-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–326（307 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% w/v PEG 3350, 0.2 M Na malate, pH 7.0	Resolution 1.60 Å R-free 0.193
8CTG Extracellular architecture of an engineered canonical Wnt signaling ternary complex Deposited 2022-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 20–629（610 aa）	Not recorded	PAM PALMITOLEIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting before plunging	Resolution 3.80 Å
8DVL Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.18 Deposited 2022-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 631–1253（623 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；0.1 M Bis-Tris 6.3, 18% PEG 10K	Resolution 2.50 Å R-free 0.245
8DVM Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.6 Deposited 2022-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 631–1253（623 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 14 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；100 mM MES pH 6.3, 12% PEG 20K	Resolution 2.00 Å R-free 0.221
8DVN Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.10 Deposited 2022-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 631–1253（623 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2 M KSCN	Resolution 2.53 Å R-free 0.246
8FFE Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide Deposited 2022-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–631（612 aa）	Not recorded	GOL GLYCEROL × 7 NA SODIUM ION × 3 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；100 mM SPG (succinate/phosphate/glycine buffer), 25% PEG 1500	Resolution 1.72 Å R-free 0.231
8S7C Ternary Complex of Cachd1, FZD5 and LRP6 Deposited 2024-02-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 629–1244（616 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.5；296 K；0.1 M Calcium Acetate 0.1 M Sodium Acetate 10% PEG 4000 pH 4.5	Resolution 4.70 Å R-free 0.261
8S7C Ternary Complex of Cachd1, FZD5 and LRP6 Deposited 2024-02-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 629–1244（616 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.5；296 K；0.1 M Calcium Acetate 0.1 M Sodium Acetate 10% PEG 4000 pH 4.5	Resolution 4.70 Å R-free 0.261
8S7C Ternary Complex of Cachd1, FZD5 and LRP6 Deposited 2024-02-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 629–1244（616 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.5；296 K；0.1 M Calcium Acetate 0.1 M Sodium Acetate 10% PEG 4000 pH 4.5	Resolution 4.70 Å R-free 0.261
9FIW MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRHFA Deposited 2024-05-29	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 1516–1521（6 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol	Resolution 2.82 Å R-free 0.246
9FIX MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRPYSYRHFA Deposited 2024-05-29	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 1516–1526（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol	Resolution 2.78 Å R-free 0.233
9FIY MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRHFA Deposited 2024-05-29	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 1521–1526（6 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol	Resolution 2.88 Å R-free 0.242

27 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LRP6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–619； UniProt 630–1246 Author chain B； PDBConstruct 3–619； UniProt 630–1246

Dickkopf-related protein 1

Homo sapiens

UniProt O94907

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 4 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 178–266	Fragment：C-terminal domain, UNP residues 178-266	Low-density lipoprotein receptor-related protein 6 × 2 （O75581） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；10-15% PEG3350, 100 mM Tris-Cl (pH 8.5), 100 mM Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.251

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3S2K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3S8V Crystal structure of LRP6-Dkk1 complex Deposited 2011-05-31	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 X 183–266（84 aa） Fragment：Dkk1c, residues 184-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；298 K；20mM citric acid, 80mM Bis-tris propane pH 8.8, 19-20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.292
3SOQ The structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1 peptide Deposited 2011-06-30	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 Z 38–44（7 aa） Fragment：UNP residues 38-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 1 GOL GLYCEROL × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M potassium thiocyanate and 30% (w/v) PEG MME 2000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.221
5FWW Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) Deposited 2016-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 182–266（85 aa） Fragment：CRD2, RESIDUES 182-266	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20 %W/V PEG3350 0.2 M NA/K-PHOSPHATE, pH 7.5	Resolution 3.50 Å R-free 0.355
5GJE Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 Deposited 2016-06-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 182–266（85 aa）	Not recorded	PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2	Resolution 21.00 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DKK1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 4–92； UniProt 178–266

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3s2k
Deposition date deposition_date	2011-05-16
Structure title title	Structural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6.
Keywords keywords	wnt co-receptor, beta-propeller, EGF domain, wnt signaling, wnt inhibitor, glycosylation, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	41.87 Å
Radius of gyration Rg (electron density) rg_electron	41.92 Å
Forward intensity I(0) i0	359078000.00
Molecular weight molecular_weight	150280.0 kDa
Excluded volume excluded_volume	186380 Å³
Envelope volume envelope_volume	249590 Å³
Hydration-shell volume shell_volume	52901 Å³
Envelope diameter envelope_diameter	171.2 Å
Shell Rg shell_rg	43.58 Å
Envelope Rg envelope_rg	41.72 Å
Shape Rg shape_rg	41.87 Å
Total Rg total_rg	42.16 Å
Total atoms total_atoms	10557
Residues n_residues	1298
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

▼

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

Maximum dimension Dmax dmax	159.3 Å
Rg (real space) rg_real	42.19 Å
Rg uncertainty (real space) rg_real_error	2.47 Å
I(0) (real space) i0_real	3.5910e+08
I(0) uncertainty (real space) i0_real_error	6.9790e+06
Rg (reciprocal space) rg_reciprocal	41.87 Å
I(0) (reciprocal space) i0_reciprocal	359000000.0000
Solution quality estimate total_estimate	0.8086
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.7 Å
Skewness Skewness skewness	0.574
Kurtosis Kurtosis kurtosis	-0.031
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	108300000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.592; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.793; Smooth: 0.938

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Low-density lipoprotein receptor-related protein 6
Molecular weight formula_weight	71475.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10613

ADPEAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVVSSVPSQNLEIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSCGEPHHHHHHHHHH

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Dickkopf-related protein 1
Molecular weight formula_weight	11114.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ADPMYHTKGQEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKHRRKGSHGLEIFQRCYCGEGLSCRIQKDHHQASNSSRLHTCQRHHHHHH

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	Spodoptera frugiperda

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

▼

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	3s2kA01
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	3s2kA02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	3s2kB01
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	3s2kB02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	3s2kC00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	80 — Lipase, subunit A
Homologous superfamily homologous superfamily	10 — Lipase, subunit A

▶

8. Citations (1)

▶

Unit-cell length a length_a	96.043 Å
Unit-cell length b length_b	108.014 Å
Unit-cell length c length_c	173.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	45.820 Å
R factor r_factor	0.1967
R_work r_work	0.1938
R_free r_free	0.2506

fit	/app/data/saxs_computation/s2/3s2k/3s2k.fit
pddf	/app/data/pr_computation/s2/3s2k/3s2k.pr.out
profile	/app/data/saxs_computation/s2/3s2k/3s2k.dat

Structural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6.

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

Low-density lipoprotein receptor-related protein 6

State in the Current Structure

Other States of the Same Protein in the Database

Dickkopf-related protein 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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)