SAXSdb — 2omz

▼

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

Internalin-A

Listeria monocytogenes

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 36–495	Fragment：internalin domain Mutation：Y369A	Epithelial-cadherin × 1 （P12830）	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

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 2OMZ	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 A 36–496（461 aa） Fragment：FUNCTIONAL DOMAIN, RESIDUES 36-496	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
1O6T Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed Deposited 2002-10-15	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 36–496（461 aa） Fragment：FUNCTIONAL DOMAIN, RESIDUES 36-496	Not recorded	MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 CL CHLORIDE ION × 4 SO4 SULFATE ION × 8 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；METHOD: VAPOUR DIFFUSION / HANGING DROP, PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.0, RESEVOIR: 10% PEG 4000, 100 MM MES/TRIS PH 6.0, 100 MM AMMONIUM SULFATE, 10 MM CACL2. CRYSTALS GREW APPROX 2 YEARS AFTER SETUP. TRUE CRYSTALLIZATION CONDITIONS PROBABLY DEVIATE FROM THOSE INDICATED	Resolution 1.60 Å R-free 0.161
1O6V Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed Deposited 2002-10-16	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 36–496（461 aa） Fragment：FUNCTIONAL DOMAIN, RESIDUES 36-496	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；METHOD: VAPOUR DIFFUSION / HANGING DROP PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.0 RESEVOIR: 10% PEG 4000, 100 MM MES/TRIS PH 6.0, 100 MM AMMONIUM SULFATE, 10 MM CACL2	Resolution 1.50 Å R-free 0.184
1O6V Internalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed Deposited 2002-10-16	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 36–496（461 aa） Fragment：FUNCTIONAL DOMAIN, RESIDUES 36-496	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；METHOD: VAPOUR DIFFUSION / HANGING DROP PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.0 RESEVOIR: 10% PEG 4000, 100 MM MES/TRIS PH 6.0, 100 MM AMMONIUM SULFATE, 10 MM CACL2	Resolution 1.50 Å R-free 0.184
2OMT Crystal structure of InlA G194S+S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–497（462 aa） Fragment：internalin domain	Mutation：G194S+S	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–497（462 aa） Fragment：internalin domain	Mutation：G194S+S Y369S	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 mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–495（460 aa） Fragment：internalin domain	Mutation：S192N Y369S	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
2OMW Crystal structure of InlA S192N Y369S/mEC1 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 A 36–496（461 aa） Fragment：internalin domain	Mutation：S192N Y369S	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
2OMX Crystal structure of InlA S192N G194S+S/hEC1 complex Deposited 2007-01-23	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–497（462 aa） Fragment：internalin domain	Mutation：S192N G194S+S	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 mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–495（460 aa） Fragment：internalin domain	Mutation：S192N	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

9 other PDB entries and 10 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 5–464； UniProt 36–495

Epithelial-cadherin

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 156–254	Fragment：N-terminal domain of human E-cadherin	Internalin-A × 1 （P25146）	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

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 2OMZ	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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
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 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 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 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 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 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
8H62 Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12 Deposited 2022-10-14	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 155–367（213 aa）	Mutation：C163S	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
9P99 CryoEM structure of integrin alphaEbeta7 bound to E-cadherin Deposited 2025-06-24	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 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 6–104； UniProt 156–254

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	2omz
Deposition date deposition_date	2007-01-23
Structure title title	Crystal structure of InlA Y369A/hEC1 complex
Keywords keywords	leucine-rich-repeat, nvasion protein, IG-like domain, adhesion protein, CELL INVASION-CELL ADHESION COMPLEX; CELL INVASION/CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	29.44 Å
Radius of gyration Rg (electron density) rg_electron	29.17 Å
Forward intensity I(0) i0	59389500.00
Molecular weight molecular_weight	61395.0 kDa
Excluded volume excluded_volume	77301 Å³
Envelope volume envelope_volume	95633 Å³
Hydration-shell volume shell_volume	29365 Å³
Envelope diameter envelope_diameter	114.2 Å
Shell Rg shell_rg	33.61 Å
Envelope Rg envelope_rg	29.77 Å
Shape Rg shape_rg	29.17 Å
Total Rg total_rg	29.58 Å
Total atoms total_atoms	4323
Residues n_residues	571
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	108.3 Å
Rg (real space) rg_real	29.72 Å
Rg uncertainty (real space) rg_real_error	1.24 Å
I(0) (real space) i0_real	5.9390e+07
I(0) uncertainty (real space) i0_real_error	1.0450e+06
Rg (reciprocal space) rg_reciprocal	29.60 Å
I(0) (reciprocal space) i0_reciprocal	59380000.0000
Solution quality estimate total_estimate	0.8021
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.642
Kurtosis Kurtosis kurtosis	0.055
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15140000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.581; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.755; Smooth: 0.929

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Internalin-A
Molecular weight formula_weight	50133.0 kDa
Mutation mutation	Y369A
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	5440

PLGSATITQDTPINQIFTDTALAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFANNKVSDVSSLANLTNINWLSAGHNQISDLTPLANLTRITQLGLNDQAWTNAPVNYKANVSIPNTVKNVTGALIAPATISDGGSYTEPDITWNLPSYTNEVSYTFSQPVTIGKGTTTFSGTVTQPLKGG

来源 Source

来源生物 organism	Listeria monocytogenes
NCBI Class编号 ncbi_taxonomy_id	169963
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Epithelial-cadherin
Molecular weight formula_weight	11523.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPLGSWVIPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQ

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	793

▼

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2omza1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.15 — Internalin Ig-like domain

Domain ID domain_id	d2omza2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.1 — Internalin LRR domain

Domain ID domain_id	d2omza3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2omza4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2omzb2
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	d2omzb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2omzb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	2omzA01
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	2omzA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1220 —

Domain ID domain_id	2omzB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

▶

8. Citations (1)

▶

Unit-cell length a length_a	55.323 Å
Unit-cell length b length_b	84.741 Å
Unit-cell length c length_c	108.416 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	1.600 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1550
R_work r_work	0.1530
R_free r_free	0.1860

fit	/app/data/saxs_computation/om/2omz/2omz.fit
pddf	/app/data/pr_computation/om/2omz/2omz.pr.out
profile	/app/data/saxs_computation/om/2omz/2omz.dat

Crystal structure of InlA Y369A/hEC1 complex

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

Epithelial-cadherin

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (7 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)