6VEL

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)
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)
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)

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)
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)
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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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
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 (202415-0)
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 (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV16	Kappa	ubiquitin-like protein, smt3,cadherin-1 chimera	SAbDab (2024-04-19)
A [auth H]	Heavy Chain	IGHV1	-	ubiquitin-like protein, smt3,cadherin-1 chimera	SAbDab (2024-04-19)

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
B [auth L]	66E8 Fab Light Chain	-	-	-
C	Ubiquitin-like protein SMT3,Cadherin-1	protein tag activity molecular tag activity protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding cytoskeletal protein binding ankyrin binding cell adhesion molecule binding cadherin binding protein tyrosine kinase binding kinase binding protein kinase binding protein tag activity molecular tag activity protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding cytoskeletal protein binding ankyrin binding cell adhesion molecule binding cadherin binding protein tyrosine kinase binding kinase binding protein kinase binding gamma-catenin binding cation binding ion binding calcium ion binding metal ion binding small molecule binding GTPase activating protein binding beta-catenin binding	organonitrogen compound metabolic process peptidyl-lysine modification primary metabolic process organic substance metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal organonitrogen compound metabolic process peptidyl-lysine modification primary metabolic process organic substance metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 inorganic substance cellular response to metal ion cellular response to lithium ion response to inorganic substance cellular response to chemical stimulus 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 cellular biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane response to toxic substance cellular component biogenesis cellular component assembly cell junction assembly cell-cell junction assembly head development forebrain development endocrine system development pituitary gland development animal organ development gland development brain development diencephalon development central nervous system development regulation of localization establishment of protein localization nitrogen compound transport nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization import into nucleus establishment of localization in cell regulation of intracellular transport positive regulation of protein localization to nucleus organic substance transport positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus establishment of localization establishment of 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 protein localization transport positive regulation of nucleocytoplasmic transport positive regulation of biological process regulation of protein localization to nucleus positive regulation of protein transport regulation of protein import into nucleus protein import into nucleus positive regulation of intracellular transport positive regulation of cellular process regulation of transport regulation of establishment of protein localization regulation of protein transport positive regulation of transport regulation of cellular localization protein transport protein localization to organelle 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 cell migration cell motility negative regulation of cell migration locomotion cell-cell adhesion via plasma-membrane adhesion molecules homophilic cell adhesion via plasma membrane adhesion molecules synapse organization synapse assembly calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules 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 organonitrogen compound catabolic process trans-synaptic signaling regulation of signaling regulation of protein metabolic process cell-cell signaling protein catabolic process regulation of catabolic process chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication organic substance catabolic process regulation of protein catabolic process cellular response to nitrogen compound response to organic substance response to alcohol response to organonitrogen compound response to endogenous stimulus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to alcohol cellular response to organonitrogen compound response to indole-3-methanol cellular response to indole-3-methanol cellular response to organic substance response to organic cyclic compound positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process 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	intracellular anatomical structure cell cortex septin ring cellular anatomical entity intracellular organelle cell periphery cytoskeleton organelle intracellular non-membrane-bounded organelle septin cytoskeleton cytoplasm non-membrane-bounded organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure cell cortex septin ring cellular anatomical entity intracellular organelle cell periphery cytoskeleton organelle intracellular non-membrane-bounded organelle septin cytoskeleton cytoplasm non-membrane-bounded organelle membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen cell projection cell leading edge plasma membrane bounded cell projection lamellipodium membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle actin cytoskeleton protein-containing complex extrinsic component of plasma membrane catenin complex plasma membrane protein complex plasma membrane membrane protein complex extrinsic component of membrane 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 endomembrane system trans-Golgi network 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
A [auth H]	66E8 Fab Heavy Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C	IPR000626	Ubiquitin-like domain	Domain
C	IPR022617	Rad60/SUMO-like domain	Domain
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

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.