SAXSdb — 8z3a

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

Sonic hedgehog protein N-product

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 29–197	Not recorded	Heavy chain of antibody 5E1 × 1 Light chain of antibody 5E1 × 1 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

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 8Z3A	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 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 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 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 ligand/ion 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 construct 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 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 experimental method Different experimental conditions 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
6N7H Cryo-EM structure of the 2:1 hPtch1-Shhp complex Deposited 2018-11-27	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 24–197（174 aa）	Not recorded	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
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 experimental method Different experimental conditions 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 method 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 oligomeric state Different ligand/ion 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 experimental method Different experimental conditions 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 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 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 experimental method Different experimental conditions 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 method 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 29–197

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8z3a
Deposition date deposition_date	2024-04-15
最后修订 last_revision	2025-04-16
Structure title title	Crystal structure of Sonic hedgehog in complex with antibody 5E1 without metals
Keywords keywords	Sonic hedgehog protein (SHH), antibody, flexible/fluctuated epitope, affinity improvement, IMMUNE SYSTEM; IMMUNE SYSTEM
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	28.88 Å
Radius of gyration Rg (electron density) rg_electron	28.51 Å
Forward intensity I(0) i0	66544300.00
Molecular weight molecular_weight	63507.0 kDa
Excluded volume excluded_volume	79155 Å³
Envelope volume envelope_volume	97782 Å³
Hydration-shell volume shell_volume	29902 Å³
Envelope diameter envelope_diameter	99.6 Å
Shell Rg shell_rg	34.42 Å
Envelope Rg envelope_rg	28.26 Å
Shape Rg shape_rg	28.46 Å
Total Rg total_rg	29.23 Å
Total atoms total_atoms	4477
Residues n_residues	574
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	94.5 Å
Rg (real space) rg_real	29.01 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	6.6540e+07
I(0) uncertainty (real space) i0_real_error	1.0930e+06
Rg (reciprocal space) rg_reciprocal	28.96 Å
I(0) (reciprocal space) i0_reciprocal	66540000.0000
Solution quality estimate total_estimate	0.8663
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	92.8 Å
Skewness Skewness skewness	0.475
Kurtosis Kurtosis kurtosis	-0.282
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12920000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.718

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Sonic hedgehog protein N-product
Molecular weight formula_weight	19122.5 kDa
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	5139

GFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Heavy chain of antibody 5E1
Molecular weight formula_weight	26318.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQSGPELVRPGVSVKISCKGSGYTFIDEALHWVKQSHAESLEWIGVIRPYSGETNYNQKFKDKATMTVDISSSTAYLELARLTSEDSAIYYCARDWERGDFFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKEQKLISEEDLNSAVDHHHHHH

来源 Source

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

Entity 3 Entity 3 polymer

Description description	Light chain of antibody 5E1
Molecular weight formula_weight	26008.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVMTQTPKFLLVSAGDKVTITCKASQSVSNDLTWYQQKPGQSPKLLIYYASNRYTGVPDRFTGSGYGTDFTFTISTVQAEDLAVYFCQQDYGSPPTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECEQKLISEEDLNSAVDHHHHHH

来源 Source

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

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	572

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8. Citations (1)

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Unit-cell length a length_a	69.370 Å
Unit-cell length b length_b	83.990 Å
Unit-cell length c length_c	126.850 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	4

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

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	50.670 Å
R factor r_factor	0.1768
R_work r_work	0.1755
R_free r_free	0.2074

fit	/app/data/saxs_computation/z3/8z3a/8z3a.fit
pddf	/app/data/pr_computation/z3/8z3a/8z3a.pr.out
profile	/app/data/saxs_computation/z3/8z3a/8z3a.dat

Crystal structure of Sonic hedgehog in complex with antibody 5E1 without metals

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

Sonic hedgehog protein N-product

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 (6)

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 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)