SAXSdb — 3lnf

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

Cadherin-1

Mus musculus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 157–369	Fragment：UNP residues 157-369 Mutation：K14E,W2A	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.2M ammonium sulfate, 0.1M Tris-Cl pH 8.5, 15% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.241
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 157–369	Fragment：UNP residues 157-369 Mutation：K14E,W2A	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.2M ammonium sulfate, 0.1M Tris-Cl pH 8.5, 15% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.241

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 3LNF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EDH E-CADHERIN DOMAINS 1 AND 2 IN COMPLEX WITH CALCIUM Deposited 1996-05-15	Different construct Different mutation/modification 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 156–380（225 aa） Chain B 156–380（225 aa）	Mutation：INS(MR-D1) Mutation：INS(MR-D1)	HG MERCURY (II) ION × 2 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；1.2 M AMMONIUM SULFATE 0.01 M CALCIUM CHLORIDE 0.1 M TRIS-HCL BUFFER, PH 9.0 0.003 M SODIUM AZIDE	Resolution 2.00 Å R-free 0.262
1FF5 STRUCTURE OF E-CADHERIN DOUBLE DOMAIN Deposited 2000-07-25	Different construct Different mutation/modification 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 157–374（218 aa） Fragment：DOUBLE DOMAIN Chain B 157–374（218 aa） Fragment：DOUBLE DOMAIN	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；50 mM ammonium sulfate, 50 mM NaOAc, 30% PEG 8000, pH 8.5, Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.93 Å
1I7W BETA-CATENIN/PHOSPHORYLATED E-CADHERIN COMPLEX Deposited 2001-03-10	Different construct Different mutation/modification 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 734–884（151 aa） Fragment：CYTOPLASMIC DOMAIN Chain D 734–884（151 aa） Fragment：CYTOPLASMIC DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；polyethylene glycol monomethylether 5000, Tris-HCl, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.245
1I7X BETA-CATENIN/E-CADHERIN COMPLEX Deposited 2001-03-10	Different construct Different mutation/modification 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 734–884（151 aa） Fragment：CYTOPLASMIC DOMAIN Chain D 734–884（151 aa） Fragment：CYTOPLASMIC DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；POLYETHYLENEIMINE TRIS-HCL ISOPROPANOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.242
1Q1P E-Cadherin activation Deposited 2003-07-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 158–369（212 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.305
1Q1P E-Cadherin activation Deposited 2003-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 158–369（212 aa）	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.305
1SUH AMINO-TERMINAL DOMAIN OF EPITHELIAL CADHERIN IN THE CALCIUM BOUND STATE, NMR, 20 STRUCTURES Deposited 1996-01-30	Different construct Different mutation/modification 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 156–300（145 aa） Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 104	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2OMW Crystal structure of InlA S192N Y369S/mEC1 complex Deposited 2007-01-23	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 B 158–256（99 aa） Fragment：N-terminal domain of murine E-cadherin	Not recorded	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；PEG 6000, LiCl, Na-Citrate, pH 5.2, vapor diffusion, hanging drop, temperature 298K	Resolution 1.85 Å R-free 0.207
2QVF mouse E-cadherin domains 1,2 Deposited 2007-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 157–369（213 aa） Fragment：Cadherin 1, Cadherin 2, UNP residues 157-369	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.286
3IFQ Interction of plakoglobin and beta-catenin with desmosomal cadherins Deposited 2009-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 778–884（107 aa） Fragment：residues 778-884 Chain D 778–884（107 aa） Fragment：residues 778-884	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289.5 K；17% PEG 3350, 0.1M Ammonium sulfate, 0.1M Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.5K	Resolution 2.80 Å R-free 0.261
3IFQ Interction of plakoglobin and beta-catenin with desmosomal cadherins Deposited 2009-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 778–884（107 aa） Fragment：residues 778-884	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289.5 K；17% PEG 3350, 0.1M Ammonium sulfate, 0.1M Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.5K	Resolution 2.80 Å R-free 0.261
3IFQ Interction of plakoglobin and beta-catenin with desmosomal cadherins Deposited 2009-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 778–884（107 aa） Fragment：residues 778-884	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289.5 K；17% PEG 3350, 0.1M Ammonium sulfate, 0.1M Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.5K	Resolution 2.80 Å R-free 0.261
3LNE Crystal structure of E-cadherin EC12 K14E Deposited 2010-02-02	Different mutation/modification 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 157–369（213 aa） Fragment：UNP residues 157-369	Mutation：K14E	CA CALCIUM ION × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES pH 6.5, 0.75M sodium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.219
3LNG Crystal structure of E-cadherin EC12 AA extension Deposited 2010-02-02	Different construct Different mutation/modification 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 157–369（213 aa） Fragment：UNP residues 157-369 Chain B 157–369（213 aa） Fragment：UNP residues 157-369	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；0.1M Tris, pH 8.5, 1.3M ammonium sulfate, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.263
3LNH Crystal structure of E-cadherin EC12 W2A Deposited 2010-02-02	Different construct Different mutation/modification 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 157–369（213 aa） Fragment：UNP residues 157-369 Chain B 157–369（213 aa） Fragment：UNP residues 157-369	Mutation：W2A Mutation：W2A	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；0.1M Tris, pH 8.5, 1.3M ammonium sulfate, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.267
3LNI Crystal structure of E-cadherin EC12 E89A Deposited 2010-02-02	Different construct Different mutation/modification 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 157–369（213 aa） Fragment：UNP residues 157-369 Chain B 157–369（213 aa） Fragment：UNP residues 157-369	Mutation：E89A Mutation：E89A	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.25M ammonium sulfate, 0.1M MES pH 6.5, 26% PEG 5000 monomethylether, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.228
3Q2L Mouse E-cadherin EC1-2 V81D mutant Deposited 2010-12-20	Different construct Different mutation/modification 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 157–369（213 aa） Fragment：E-cadherin EC1-2 fragment, residues 157-369 Chain B 157–369（213 aa） Fragment：E-cadherin EC1-2 fragment, residues 157-369	Mutation：V81D Mutation：V81D	CA CALCIUM ION × 8 1PE PENTAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；10% (v/v) PEG 400, 0.1M sodium acetate pH4.6, 0.13M CaCl2, Cryoprotected by increasing PEG 400 to 30%, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.245
3Q2N Mouse E-cadherin EC1-2 L175D mutant Deposited 2010-12-20	Different construct Different mutation/modification 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 157–369（213 aa） Fragment：E-cadherin EC1-2 fragment, residues 157-369 Chain B 157–369（213 aa） Fragment：E-cadherin EC1-2 fragment, residues 157-369	Mutation：L175D Mutation：L175D	CA CALCIUM ION × 8 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% (v/v) PEG 400, 0.1M sodium acetate pH4.6, 0.15M CaCl2 and croprotected by increasing PEG 400 to 30%., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.73 Å R-free 0.224
3Q2V Crystal structure of mouse E-cadherin ectodomain Deposited 2010-12-20	Different construct Different mutation/modification 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 157–700（544 aa） Fragment：UNP residues 157-700 Chain B 157–700（544 aa） Fragment：UNP residues 157-700	Not recorded	CA CALCIUM ION × 24 MN MANGANESE (II) ION × 2 MAN alpha-D-mannopyranose × 18	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；11% (w/v) PEG 5000 monomethyl ether (MME), 0.1M Bicine pH 8.5, 10mM CaCl2, 30mM MnCl2, 2% (v/v) dioxane, 4% (v/v) 1-butanol , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.293
3QRB crystal structure of E-cadherin EC1-2 P5A P6A Deposited 2011-02-17	Different construct Different mutation/modification 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 157–369（213 aa） Fragment：Cadherin 1 and Cadherin 2 Domains, UNP residues 157-369	Mutation：P161A, P162A	CA CALCIUM ION × 6 EDO 1,2-ETHANEDIOL × 4 PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG8000, 10% ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.178
3QRB crystal structure of E-cadherin EC1-2 P5A P6A Deposited 2011-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 157–369（213 aa） Fragment：Cadherin 1 and Cadherin 2 Domains, UNP residues 157-369	Mutation：P161A, P162A	CA CALCIUM ION × 6 EDO 1,2-ETHANEDIOL × 4 PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% PEG8000, 10% ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.178
4QD2 Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex Deposited 2014-05-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 157–369（213 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Tris (pH8.0), 6% PEG8000, 200mM potassium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.247
4QD2 Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex Deposited 2014-05-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 157–369（213 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Tris (pH8.0), 6% PEG8000, 200mM potassium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.247
7AR4 Crystal structure of beta-catenin in complex with cyclic peptide inhibitor Deposited 2020-10-23	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 PaP 783–798（16 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M HEPES, 4% PEG6000, 20 mM TRIS, 150 mM NaCl, 0.5 % Glycerol, 2 mM DTT	Resolution 2.60 Å R-free 0.242

19 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CADH1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–213； UniProt 157–369 Author chain B； PDBConstruct 1–213； UniProt 157–369

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	3lnf
Deposition date deposition_date	2010-02-02
Structure title title	Crystal structure of E-cadherin EC12 K14EW2A
Keywords keywords	cadherin, Calcium, Cell adhesion, Cell junction, Cell membrane, Glycoprotein, Transmembrane; CELL ADHESION
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	29.04 Å
Radius of gyration Rg (electron density) rg_electron	28.63 Å
Forward intensity I(0) i0	34358100.00
Molecular weight molecular_weight	45349.0 kDa
Excluded volume excluded_volume	56561 Å³
Envelope volume envelope_volume	72052 Å³
Hydration-shell volume shell_volume	22350 Å³
Envelope diameter envelope_diameter	97.8 Å
Shell Rg shell_rg	33.73 Å
Envelope Rg envelope_rg	28.52 Å
Shape Rg shape_rg	28.65 Å
Total Rg total_rg	29.10 Å
Total atoms total_atoms	3182
Residues n_residues	416
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	94.2 Å
Rg (real space) rg_real	29.16 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	3.4360e+07
I(0) uncertainty (real space) i0_real_error	5.5350e+05
Rg (reciprocal space) rg_reciprocal	29.11 Å
I(0) (reciprocal space) i0_reciprocal	34360000.0000
Solution quality estimate total_estimate	0.8728
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.3 Å
Skewness Skewness skewness	0.408
Kurtosis Kurtosis kurtosis	-0.343
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1391000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.731

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cadherin-1
Molecular weight formula_weight	23145.7 kDa
Mutation mutation	K14E,W2A
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	3351

DAVIPPISCPENEEGEFPKNLVQIKSNRDKETKVFYSITGQGADKPPVGVFIIERETGWLKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAEGAVPGTSVMKVSATDADDDVNTYNAAIAYTIVSQDPELPHKNMFTVNRDTGVISVLTSGLDRESYPTYTLVVQAADLQGEGLSTTAKAVITVKD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3lnfa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

Domain ID domain_id	d3lnfa2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

Domain ID domain_id	d3lnfb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

Domain ID domain_id	d3lnfb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

CATH v4.4 (4 domains)

Domain ID domain_id	3lnfA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	3lnfA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	3lnfB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	3lnfB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

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8. Citations (1)

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Unit-cell length a length_a	45.107 Å
Unit-cell length b length_b	47.383 Å
Unit-cell length c length_c	69.897 Å
Unit-cell angle α angle_alpha	70.58 °
Unit-cell angle β angle_beta	88.13 °
Unit-cell angle γ angle_gamma	75.50 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	28.635 Å
R factor r_factor	0.1872
R_work r_work	0.1842
R_free r_free	0.2408

fit	/app/data/saxs_computation/ln/3lnf/3lnf.fit
pddf	/app/data/pr_computation/ln/3lnf/3lnf.pr.out
profile	/app/data/saxs_computation/ln/3lnf/3lnf.dat

Crystal structure of E-cadherin EC12 K14EW2A

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

Cadherin-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