SAXSdb — 8h62

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

Internalin A

Listeria monocytogenes serovar 1/2a

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 36–496	Not recorded	Cadherin-1 × 1 （P12830） CA CALCIUM ION × 4 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium acetate 45% MPD	Resolution 1.91 Å R-free 0.210

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 8H62	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8H63 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound Deposited 2022-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–496（461 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 IPA ISOPROPYL ALCOHOL × 1 GOL GLYCEROL × 2 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.085 M HEPES sodium pH 7.0; 8.5% Isopropanol; 20% PEG 4,000	Resolution 1.53 Å R-free 0.190
8H64 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound Deposited 2022-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–496（461 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000	Resolution 2.35 Å R-free 0.227
8H64 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound Deposited 2022-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 36–496（461 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000	Resolution 2.35 Å R-free 0.227
8H64 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound Deposited 2022-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 36–496（461 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000	Resolution 2.35 Å R-free 0.227
8H64 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound Deposited 2022-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 36–496（461 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000	Resolution 2.35 Å R-free 0.227

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	INLA_LISMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–462； UniProt 36–496

Cadherin-1

Homo sapiens

UniProt P12830

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 155–367	Mutation：C163S	Internalin A × 1 （P0DJM0） CA CALCIUM ION × 4 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium acetate 45% MPD	Resolution 1.91 Å R-free 0.210

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 8H62	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1O6S Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognition Complex Deposited 2002-10-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–255（100 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 156-253	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；VAPOUR DIFFUSION / HANGING DROP 10 MG/ML IN 10 MM HEPES PH 7.0, 26% PEG 4000, 100 MM MES/TRIS PH 7.0, 100 MM SODIUM ACETATE, 50 MM CACL2	Resolution 1.80 Å R-free 0.221
2O72 Crystal Structure Analysis of human E-cadherin (1-213) Deposited 2006-12-09	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 155–367（213 aa） Fragment：N-Terminal domains 1 and 2, residues 155-317	Mutation：C9S	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG 8000, 0.2M calcium chloride, 5% DMSO, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K, temperature 277K	Resolution 2.00 Å R-free 0.234
2OMT Crystal structure of InlA G194S+S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–255（100 aa） Fragment：N-terminal domain of human E-cadherin	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 2.00 Å R-free 0.283
2OMU Crystal structure of InlA G194S+S Y369S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–255（100 aa） Fragment：N-terminal domain of human E-cadherin	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.80 Å R-free 0.217
2OMV Crystal structure of InlA S192N Y369S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–255（100 aa） Fragment：N-terminal domain of human E-cadherin	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.90 Å R-free 0.219
2OMX Crystal structure of InlA S192N G194S+S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–258（103 aa） Fragment：N-terminal domain of human E-cadherin	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.70 Å R-free 0.223
2OMY Crystal structure of InlA S192N/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–254（99 aa） Fragment：N-terminal domain of human E-cadherin	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.70 Å R-free 0.211
2OMZ Crystal structure of InlA Y369A/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–254（99 aa） Fragment：N-terminal domain of human E-cadherin	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.60 Å R-free 0.186
3FF7 Structure of NK cell receptor KLRG1 bound to E-cadherin Deposited 2008-12-02	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 A 155–253（99 aa） Fragment：UNP residues 155-253, Cadherin 1 domain Chain B 155–253（99 aa） Fragment：UNP residues 155-253, Cadherin 1 domain	Mutation：C9L Mutation：C9L	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；298 K；PEG4000, pH 4.6, vapor diffusion, temperature 298K	Resolution 1.80 Å R-free 0.246
3FF8 Structure of NK cell receptor KLRG1 bound to E-cadherin Deposited 2008-12-02	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 A 155–254（100 aa） Fragment：UNP residues 155-254, Cadherin 1 domain Chain B 155–254（100 aa） Fragment：UNP residues 155-254, Cadherin 1 domain	Mutation：C9L Mutation：C9L	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；PEG8000, pH 6.5, vapor diffusion, temperature 298K	Resolution 2.00 Å R-free 0.253
4ZT1 Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation Deposited 2015-05-14	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 157–367（211 aa） Fragment：UNP residues 157-367 Chain B 157–367（211 aa） Fragment：UNP residues 157-367	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；TRIS 0.1 M, ammonium sulfate 1.3 M, calcium chloride 50 mM	Resolution 1.92 Å R-free 0.219
4ZTE Crystal structure of human E-Cadherin (residues 3-213) in complex with a peptidomimetic inhibitor Deposited 2015-05-14	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 157–367（211 aa） Fragment：residues 157-367 Chain B 157–367（211 aa） Fragment：residues 157-367	Not recorded	CA CALCIUM ION × 6 4RL N-{[(2S,5S)-1-benzyl-5-(2-{[(2S,3S)-1-(tert-butylamino)-3-methyl-1-oxopentan-2-yl]amino}-2-oxoethyl)-3,6-dioxopiperazin-2-yl]methyl}-L-alpha-asparagine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；TRIS 0.1 M, ammonium sulfate 1.3 M, calcium chloride 80 mM	Resolution 2.13 Å R-free 0.230
6CXY Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11 Deposited 2018-04-04	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 C 155–371（217 aa）	Not recorded	CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 18 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；HosaA.19747.a.KW2.PC00156 at 10.3 mg/ml in a buffer containing 50 mM Tris, pH = 8, 150 mM NaCl, and 3 mM CaCl2 was mixed 0.1 uL + 0.1 uL with Wizard 3/4 (h12): 15% (w/v) PEG-20,000, 0.1 M HEPES/ NaOH, pH = 7.0. The crystal was cryoprotected with 20% ethylene glycol. Tray: 299140h12, puck: qxp2-3	Resolution 2.20 Å R-free 0.197
6OLE Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs Deposited 2019-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric	Chain y 693–730（38 aa）	Not recorded	MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6OLF Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAs Deposited 2019-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric	Chain y 693–730（38 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 31 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6OLG Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA) Deposited 2019-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric	Chain A 693–730（38 aa）	Not recorded	MG MAGNESIUM ION × 326 ZN ZINC ION × 5 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6VEL Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab Deposited 2020-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 155–371（217 aa）	Not recorded	SO4 SULFATE ION × 6 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；A complex of HosaA.19747.a.KW2, MumuA.20194.a.LG23, and MumuA.20195.a.LH23 was crystallized at 10.4 mg/ml at 14C and mixed 1:1 with 12.5% (w/v) PEG 4000, 20% (v/v) 1,2,6-hexanetriol, 0.1M GlyGly/AMPD pH 8.5, 0.03M of each Lithium sulfate, Sodium sulfate, and Potassium sulfate. Tray 307437a10: puck ckt8-9.	Resolution 2.65 Å R-free 0.236
7STZ Crystal Structure of Human E-cadherin EC1-5 bound by mouse monoclonal antibody Fab mAb-1_19A11 Deposited 2021-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 155–698（544 aa） Chain D 155–698（544 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PG4 TETRAETHYLENE GLYCOL × 5 MAN alpha-D-mannopyranose × 3 BMA beta-D-mannopyranose × 12 CA CALCIUM ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；HosaA.19747.a.LS31.PC00180 at 11.5 mg/mL was mixed 2:1 (0.2 uL protein and 0.1 uL precipitant) with 0.1M sodium HEPES pH 7.0 and 15% w/v PEG4000 (ProPlex B11) and stored at 14C. The crystal was cryoprotected with 15% ethylene glycol. Tray: 321285b11, puck: ygq5-2.	Resolution 2.95 Å R-free 0.208
9P99 CryoEM structure of integrin alphaEbeta7 bound to E-cadherin Deposited 2025-06-24	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 C 155–371（217 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å

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

View Construct and Data Evidence

UniProt name	CADH1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–213； UniProt 155–367

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	8h62
Deposition date deposition_date	2022-10-14
Structure title title	Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12
Keywords keywords	Internalin A Cadherin Bacterial invasion nanobody Surface plasmon resonance Isothermal titration calorimetry, CELL INVASION; CELL INVASION
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	32.94 Å
Radius of gyration Rg (electron density) rg_electron	32.88 Å
Forward intensity I(0) i0	83800700.00
Molecular weight molecular_weight	73178.0 kDa
Excluded volume excluded_volume	91868 Å³
Envelope volume envelope_volume	115380 Å³
Hydration-shell volume shell_volume	32090 Å³
Envelope diameter envelope_diameter	128.2 Å
Shell Rg shell_rg	35.84 Å
Envelope Rg envelope_rg	33.21 Å
Shape Rg shape_rg	32.89 Å
Total Rg total_rg	33.10 Å
Total atoms total_atoms	5144
Residues n_residues	675
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	121.2 Å
Rg (real space) rg_real	33.21 Å
Rg uncertainty (real space) rg_real_error	1.27 Å
I(0) (real space) i0_real	8.3800e+07
I(0) uncertainty (real space) i0_real_error	1.3630e+06
Rg (reciprocal space) rg_reciprocal	33.09 Å
I(0) (reciprocal space) i0_reciprocal	83790000.0000
Solution quality estimate total_estimate	0.8321
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.3 Å
Skewness Skewness skewness	0.502
Kurtosis Kurtosis kurtosis	-0.141
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8674000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.720; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.714; Smooth: 0.937

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Internalin A
Molecular weight formula_weight	49914.8 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	5815

SATITQDTPINQIFTDTALAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFYNNKVSDVSSLANLTNINWLSAGHNQISDLTPLANLTRITQLGLNDQAWTNAPVNYKANVSIPNTVKNVTGALIAPATISDGGSYTEPDITWNLPSYTNEVSYTFSQPVTIGKGTTTFSGTVTQPLKA

来源 Source

来源生物 organism	Listeria monocytogenes serovar 1/2a
NCBI Class编号 ncbi_taxonomy_id	169963
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Cadherin-1
Molecular weight formula_weight	23134.7 kDa
Mutation mutation	C163S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DWVIPPISSPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTD

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

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	630

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8. Citations (1)

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Unit-cell length a length_a	55.350 Å
Unit-cell length b length_b	69.580 Å
Unit-cell length c length_c	72.490 Å
Unit-cell angle α angle_alpha	101.48 °
Unit-cell angle β angle_beta	97.77 °
Unit-cell angle γ angle_gamma	105.99 °
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	1.910 Å
Low-resolution limit resolution_low	34.800 Å
R factor r_factor	0.1776
R_work r_work	0.1763
R_free r_free	0.2097

fit	/app/data/saxs_computation/h6/8h62/8h62.fit
pddf	/app/data/pr_computation/h6/8h62/8h62.pr.out
profile	/app/data/saxs_computation/h6/8h62/8h62.dat

Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12

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

Internalin A

State in the Current Structure

Other States of the Same Protein in the Database

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)