SAXSdb — 6n7h

▼

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

Protein patched homolog 1

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 2 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–1305 Chain B； UniProt 1–1305	Not recorded	Sonic hedgehog protein × 1 （Q15465） 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 × 10 CLR CHOLESTEROL × 5 ZN ZINC ION × 1 CA CALCIUM ION × 2 PLM PALMITIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

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 6N7H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6DMB Cryo-EM structure of human Ptch1 Deposited 2018-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6DMO Cryo-EM structure of human Ptch1 with three mutations L282Q/T500F/P504L Deposited 2018-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1305（1305 aa）	Mutation：L282Q, T500F, P504L	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6DMY Cryo-EM structure of human Ptch1 and ShhN complex Deposited 2018-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 2 SER SERINE × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6E1H Structure of 2:1 human Ptch1-Shh-N complex Deposited 2018-07-09	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 A 1–1447（1447 aa） Chain B 1–1447（1447 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2 PLM PALMITIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 3.50 Å
6N7G Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form I) Deposited 2018-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–1305（1305 aa） Chain B 1–1305（1305 aa） Chain D 1–1305（1305 aa） Chain E 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 CLR CHOLESTEROL × 10 ZN ZINC ION × 2 CA CALCIUM ION × 4 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.80 Å
6N7K Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form II) Deposited 2018-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–1305（1305 aa） Chain B 1–1305（1305 aa） Chain D 1–1305（1305 aa） Chain E 1–1305（1305 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 CLR CHOLESTEROL × 10 ZN ZINC ION × 2 CA CALCIUM ION × 4 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
6OEU Structure of human Patched1 Deposited 2019-03-27	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 1–1447（1447 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 3.50 Å
6OEV Structure of human Patched1 in complex with native Sonic Hedgehog Deposited 2019-03-27	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 1–1447（1447 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 3.80 Å
6RMG Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II Deposited 2019-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1189（1189 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 11 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6RTW Crystal structure of the Patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and cholesterol-hemisuccinate Deposited 2019-05-27	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 × 2 PDB declaration: dimeric	Chain A 136–423（288 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 Y01 CHOLESTEROL HEMISUCCINATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES/MOPS pH 7.5, 0.03 M of each halide (sodium fluoride, sodium bromide, sodium iodide), 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350	Resolution 1.90 Å R-free 0.230
6RTX Crystal structure of the Patched-1 (PTCH1) ectodomain 1 Deposited 2019-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 139–428（290 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M bicine/Trizma base pH 8.5, 0.03M of each ethylene glycol (diethyleneglycol, triethyleneglycol, tetraethyleneglycol and pentaethyleneglycol), 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350	Resolution 1.95 Å R-free 0.257
6RTY Crystal structure of the Patched ectodomain in complex with nanobody NB64 Deposited 2019-05-27	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 × 2 PDB declaration: dimeric	Chain A 136–423（288 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES/imidazole pH 6.5, 0.02M of each amino acid (L-glutamate, alanine, glycine, lysine, serine), 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350	Resolution 2.10 Å R-free 0.255
6RVC Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75 Deposited 2019-05-31	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 × 2 PDB declaration: dimeric	Chain A 772–1023（252 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M sodium nitrate, 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.241
6RVC Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75 Deposited 2019-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 772–1023（252 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M sodium nitrate, 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.241
6RVC Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75 Deposited 2019-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 772–1023（252 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M sodium nitrate, 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.241
6RVD Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex Deposited 2019-05-31	Different construct 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 1–1447（1447 aa） Chain B 1–1447（1447 aa）	Not recorded	CLR CHOLESTEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 PLM PALMITIC ACID × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 0.06% Digitonin, 1mM CaCl2. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9MS8 PTCH1 in complex with Fab6H3 Deposited 2025-01-09	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 A 1–618（618 aa） Chain A 721–1188（468 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å

15 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–1326； UniProt 1–1305 Author chain B； PDBConstruct 22–1326； UniProt 1–1305

Sonic hedgehog protein

Homo sapiens

UniProt Q15465

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 2 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 24–197	Not recorded	Protein patched homolog 1 × 2 （Q13635） 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 × 10 CLR CHOLESTEROL × 5 ZN ZINC ION × 1 CA CALCIUM ION × 2 PLM PALMITIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.60 Å

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 6N7H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3HO5 Crystal structure of Hedgehog-interacting protein (HHIP) and Sonic hedgehog (SHH) complex Deposited 2009-06-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 29–197（169 aa） Fragment：UNP residues 29-197	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M bis-Tris propane pH 7.0 and 2.2-2.5 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.01 Å R-free 0.287
3M1N Crystal structure of Human Sonic Hedgehog N-terminal domain Deposited 2010-03-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–197（175 aa） Fragment：Sonic hedgehog protein N-product	Mutation：A23I, C24I	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；21-24% PEG 4000, 200 mM LiSO4, and 100 mM Tris, pH = 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.85 Å R-free 0.260
3M1N Crystal structure of Human Sonic Hedgehog N-terminal domain Deposited 2010-03-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–197（175 aa） Fragment：Sonic hedgehog protein N-product	Mutation：A23I, C24I	ZN ZINC ION × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；21-24% PEG 4000, 200 mM LiSO4, and 100 mM Tris, pH = 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.85 Å R-free 0.260
3MXW Crystal structure Sonic hedgehog bound to the 5E1 fab fragment Deposited 2010-05-07	Different construct 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 A 29–197（169 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；protein solution (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volume of well solution (0.2 M lithium sulfate, 100 mM Hepes, pH 7.5, and 22% w/v PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.83 Å R-free 0.218
6DMY Cryo-EM structure of human Ptch1 and ShhN complex Deposited 2018-06-05	Different oligomeric state Different ligand/ion	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–197（174 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 2 SER SERINE × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6E1H Structure of 2:1 human Ptch1-Shh-N complex Deposited 2018-07-09	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 24–197（174 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2 PLM PALMITIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 3.50 Å
6N7G Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form I) Deposited 2018-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 24–197（174 aa） Chain F 24–197（174 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 CLR CHOLESTEROL × 10 ZN ZINC ION × 2 CA CALCIUM ION × 4 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.80 Å
6N7K Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form II) Deposited 2018-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 24–197（174 aa） Chain F 24–197（174 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 CLR CHOLESTEROL × 10 ZN ZINC ION × 2 CA CALCIUM ION × 4 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
6OEV Structure of human Patched1 in complex with native Sonic Hedgehog Deposited 2019-03-27	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 C 23–197（175 aa） Fragment：residues 24-197	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7	Resolution 3.80 Å
6PJV Structure of Human Sonic Hedgehog in complex with Zinc and Magnesium Deposited 2019-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–197（169 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 3 GOL GLYCEROL × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；24% (w/v) polyethylene glycol 8000, 0.10 M TRIS pH 7.0, and 0.24 M MgCl2	Resolution 1.43 Å R-free 0.139
6RMG Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II Deposited 2019-05-06	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 21–197（177 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 11 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6RVD Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex Deposited 2019-05-31	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 24–197（174 aa）	Not recorded	CLR CHOLESTEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 PLM PALMITIC ACID × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes pH 7.5, 150 mM NaCl, 0.06% Digitonin, 1mM CaCl2. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7E2I Cryo-EM structure of hDisp1NNN-ShhN Deposited 2021-02-05	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–462（462 aa）	Not recorded	ZN ZINC ION × 1 Y01 CHOLESTEROL HEMISUCCINATE × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.07 Å
7MHZ Human Hedgehog acyltransferase (HHAT) in complex with a palmitoylated Hedgehog peptide product and a Fab antibody fragment Deposited 2021-04-16	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 24–31（8 aa） Fragment：UNP residues 24-31	Not recorded	PLM PALMITIC ACID × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 PKZ Palmitoyl-CoA × 3 AJP Digitonin × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7RHQ Cryo-EM structure of Xenopus Patched-1 in complex with GAS1 and Sonic Hedgehog Deposited 2021-07-18	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 24–197（174 aa）	Not recorded	CLR CHOLESTEROL × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 CA CALCIUM ION × 2 PLM PALMITIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.53 Å
8YYZ Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A in the absence of metals Deposited 2024-04-04	Different construct 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 A 29–197（169 aa）	Not recorded	CL CHLORIDE ION × 5 GOL GLYCEROL × 1 IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M Ammonium iodide, 20% w/v Polyethylene glycol 3350	Resolution 1.90 Å R-free 0.222
8Z2V Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A with metals Deposited 2024-04-13	Different construct 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 A 29–197（169 aa）	Not recorded	CL CHLORIDE ION × 1 ZN ZINC ION × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；200mM MgCl2, 20% PEG 3350	Resolution 1.89 Å R-free 0.225
8Z39 Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant L-T56A with metals Deposited 2024-04-14	Different construct 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 A 29–197（169 aa）	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；200mM NaCl, 20% PEG 3350	Resolution 1.80 Å R-free 0.208
8Z3A Crystal structure of Sonic hedgehog in complex with antibody 5E1 without metals Deposited 2024-04-15	Different construct 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 A 29–197（169 aa）	Not recorded	GOL GLYCEROL × 1 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；200mM KNO3, 20% PEG 3350	Resolution 1.75 Å R-free 0.207

18 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SHH_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–174； UniProt 24–197

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6n7h
Deposition date deposition_date	2018-11-27
Structure title title	Cryo-EM structure of the 2:1 hPtch1-Shhp complex
Keywords keywords	Receptor, RND family, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	49.04 Å
Radius of gyration Rg (electron density) rg_electron	48.45 Å
Forward intensity I(0) i0	758797000.00
Molecular weight molecular_weight	244480.0 kDa
Excluded volume excluded_volume	311820 Å³
Envelope volume envelope_volume	450440 Å³
Hydration-shell volume shell_volume	74153 Å³
Envelope diameter envelope_diameter	156.9 Å
Shell Rg shell_rg	56.65 Å
Envelope Rg envelope_rg	47.19 Å
Shape Rg shape_rg	48.43 Å
Total Rg total_rg	48.82 Å
Total atoms total_atoms	17242
Residues n_residues	2153
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	153.2 Å
Rg (real space) rg_real	48.83 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	7.5880e+08
I(0) uncertainty (real space) i0_real_error	1.3670e+07
Rg (reciprocal space) rg_reciprocal	49.04 Å
I(0) (reciprocal space) i0_reciprocal	759000000.0000
Solution quality estimate total_estimate	0.8942
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	71.8 Å
Skewness Skewness skewness	0.063
Kurtosis Kurtosis kurtosis	-0.757
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	102200000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.778

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Protein patched homolog 1
Molecular weight formula_weight	150189.6 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	17242

MADYKDDDDKSGPDEVDASGRMASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGLRRAAAPDRDYLHRPSYCDAAFALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCGKFLVVGLLIFGAFAVGLKAANLETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTTEALLQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQIIEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWEEMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVLSFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLRWDCSKSQGAVGLAGVLLVALSVAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLAHAFSETGQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAVVVVFNFAMVLLIFPAILSMDLYRREDRRLDIFCCFTSPCVSRVIQVEPQAYTDTHDNTRYSPPPPYSSHSFAHETQITMQSTVQLRTEYDPHTHVYYTTAEPRSEISVQPVTVTQDTLSCQSPESTSSTRDLLSQFSDSSLHCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLGLLGVSLYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLLYDLHRSFSNVKYVMLEENKQLPKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDDGVLAYKLLVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQANIRPHRPEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICSNYTSLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMVLALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLALEHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFGPYPEVSPANGLNRLPTPSPEPPPSVVRFAMPPGHTHSGSDSSDSEYSSQTTVSGLSEELRHYEAQQGAGGPAHQVIVEATENPVFAHSTVVHPESRHHPPSNPRQQPHLDSGSLPPGRQGQQPRRDLEGSDEVDAVEGSHHHHHHHHHH

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Sonic hedgehog protein
Molecular weight formula_weight	19594.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

CGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

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	Homo sapiens

Entity 3 Entity 3 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	nat
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	nat
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6n7hC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	10 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	171590

fit	/app/data/saxs_computation/n7/6n7h/6n7h.fit
pddf	/app/data/pr_computation/n7/6n7h/6n7h.pr.out
profile	/app/data/saxs_computation/n7/6n7h/6n7h.dat

Cryo-EM structure of the 2:1 hPtch1-Shhp complex

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

Protein patched homolog 1

State in the Current Structure

Other States of the Same Protein in the Database

Sonic hedgehog protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (8)

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 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

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)