6VEL | pdb_00006vel

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth H]	d6velh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth L]	d6vell2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth L]	d6vell1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Cadherin-like	8055235	3002049	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth H]	V-set_8	e6velH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A [auth H]	C1-set_1	e6velH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B [auth L]	C1-set_4	e6velL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e6velL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C	Cadherin	e6velC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Cadherin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	2.60.40.60	Mainly Beta	Sandwich	Immunoglobulin-like	Cadherins	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth H]	Fab 66E8, anti-CDH1	VH-CH1	Homo sapiens (human)	IGHV1-3701, IGHJ201, IGHG1*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202546-0)
B [auth L]	Fab 66E8, anti-CDH1	L-KAPPA	Homo sapiens (human)	IGKV16-10401, IGKJ101, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV1	-	ubiquitin-like protein, smt3,cadherin-1 chimera	SAbDab (2025-11-28)
B [auth L]	Light Chain	IGKV16	Kappa	ubiquitin-like protein, smt3,cadherin-1 chimera	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00028	Cadherin domain (Cadherin)	Cadherin domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H]	66E8 Fab Heavy Chain	-	-	-
B [auth L]	66E8 Fab Light Chain	-	-	-
C	Ubiquitin-like protein SMT3,Cadherin-1	cytoskeletal protein binding ankyrin binding protein binding binding cell adhesion molecule binding cadherin binding protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding identical protein binding gamma-catenin binding cation binding ion binding cytoskeletal protein binding ankyrin binding protein binding binding cell adhesion molecule binding cadherin binding protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding identical protein binding gamma-catenin binding cation binding ion binding calcium ion binding metal ion binding small molecule binding GTPase activating protein binding beta-catenin binding protein tag activity molecular tag activity ubiquitin-like protein ligase binding	response to stimulus response to chemical response to xenobiotic stimulus adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to lithium ion cellular response to lithium ion response to stimulus response to chemical response to xenobiotic stimulus adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to lithium ion cellular response to lithium ion response to metal ion axon extension multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size developmental growth cell projection organization negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation anatomical structure development regulation of biological quality system development developmental process regulation of biological process negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth nervous system development developmental growth involved in morphogenesis generation of neurons negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension regulation of nervous system development neurogenesis negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process biological regulation growth negative regulation of axon extension axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane response to toxic substance cell migration cell motility cellular component biogenesis cellular component assembly cell junction assembly cell-cell junction assembly head development forebrain development endocrine system development pituitary gland development gland development animal organ development brain development diencephalon development central nervous system development regulation of localization establishment of protein localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of biological process positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport import into nucleus regulation of protein import into nucleus establishment of localization in cell protein import into nucleus positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport regulation of transport positive regulation of protein localization to nucleus regulation of establishment of protein localization positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization establishment of protein localization to organelle positive regulation of transport protein transport regulation of cellular localization protein localization to organelle positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport regulation of cell adhesion negative regulation of cell adhesion cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion regulation of cell-cell adhesion negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility negative regulation of cell migration locomotion homophilic cell-cell adhesion synapse organization synapse assembly calcium-dependent cell-cell adhesion response to heparin response to oxygen-containing compound response to nitrogen compound desmosome organization desmosome assembly cell-cell adhesion mediated by cadherin catabolic process modulation of chemical synaptic transmission signaling macromolecule catabolic process regulation of protein catabolic process at postsynapse, modulating synaptic transmission regulation of primary metabolic process cell communication synaptic signaling postsynaptic modulation of chemical synaptic transmission protein metabolic process trans-synaptic signaling regulation of signaling regulation of protein metabolic process cell-cell signaling primary metabolic process protein catabolic process regulation of catabolic process chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of protein catabolic process cellular response to nitrogen compound response to alcohol cellular response to oxygen-containing compound cellular response to alcohol response to indole-3-methanol cellular response to indole-3-methanol positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus response to Gram-positive bacterium peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton cell periphery protein-containing complex extrinsic component of plasma membrane catenin complex plasma membrane protein complex plasma membrane membrane protein complex extrinsic component of membrane cytoplasm membrane raft plasma membrane raft caveola membrane microdomain flotillin complex plasma membrane region synapse cell junction glutamatergic synapse apical junction complex cell-cell junction anchoring junction adherens junction Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system trans-Golgi network desmosome perinuclear region of cytoplasm postsynapse endosome intracellular vesicle cytoplasmic vesicle lateral plasma membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane cell cortex septin ring septin cytoskeleton condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR014868	Cadherin prodomain	Domain
C	IPR027397	Catenin binding domain superfamily	Homologous Superfamily
C	IPR015919	Cadherin-like superfamily	Homologous Superfamily
C	IPR039808	Cadherin	Family
C	IPR002126	Cadherin-like	Domain
C	IPR000233	Cadherin, Y-type LIR-motif	Domain
C	IPR020894	Cadherin conserved site	Conserved Site
C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C	IPR000626	Ubiquitin-like domain	Domain
C	IPR022617	Rad60/SUMO-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P12830	ulcerative colitis ovarian cancer prostate cancer squamous cell carcinoma colorectal cancer invasive ductal breast carcinoma endometrial cancer hereditary diffuse gastric adenocarcinoma Neoplasms, Experimental adenoid cystic carcinoma blepharocheilodontic syndrome cancer urinary bladder cancer familial prostate carcinoma breast carcinoma ulcerative colitis ovarian cancer prostate cancer squamous cell carcinoma colorectal cancer invasive ductal breast carcinoma endometrial cancer hereditary diffuse gastric adenocarcinoma Neoplasms, Experimental adenoid cystic carcinoma blepharocheilodontic syndrome cancer urinary bladder cancer familial prostate carcinoma breast carcinoma hereditary breast carcinoma carcinoma invasive lobular breast carcinoma endometrial carcinoma gastric cancer prostate intraepithelial neoplasia salivary gland adenoid cystic carcinoma breast cancer sarcomatoid carcinoma urinary bladder neoplasm intestinal disease kidney disease non-small cell lung carcinoma cutaneous melanoma ductal breast carcinoma in situ lung adenocarcinoma ovarian carcinoma lung disease pancreatic neoplasm atypical teratoid rhabdoid tumor salivary gland cancer Helicobacter pylori infectious disease mammary neoplasms, animal medulloblastoma thyroid gland carcinoma uterine disease liver disease osteosarcoma lung cancer ovarian disease malignant glioma pilocytic astrocytoma primitive neuroectodermal tumor gastric carcinoma benign mesothelioma prostate disease psoriasis gastrointestinal stromal tumor blepharocheilodontic syndrome 1 hematologic disease stomach carcinoma in situ mesothelioma urinary bladder disease interstitial cystitis colorectal carcinoma connective tissue disease lung carcinoma ovarian neoplasm malignant mesothelioma precancerous condition gastric neoplasm malignant pancreatic neoplasm benign neoplasm of stomach breast disease stomach disease mouth disease undifferentiated carcinoma colorectal adenoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.