5JYM | pdb_00005jym

Human P-cadherin EC12 with scFv TSP11 bound

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d5jymd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d5jymd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5jymb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5jymb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d5jymc1	All beta proteins	Immunoglobulin-like beta-sandwich	Cadherin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5jyma1	All beta proteins	Immunoglobulin-like beta-sandwich	Cadherin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	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	8074074	3002049	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cadherin-like	8074074	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)
D	V-set_8	e5jymD2	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)
D	V-set	e5jymD1	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)
B	V-set_8	e5jymB1	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)
B	V-set	e5jymB2	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	e5jymC1	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	Cadherin	e5jymA1	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)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	2.60.40.60	Mainly Beta	Sandwich	Immunoglobulin-like	Cadherins	CATH (4.3.0)
A	2.60.40.60	Mainly Beta	Sandwich	Immunoglobulin-like	Cadherins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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, D	Antibody scFv TSP11	-	-	-
A, C	Cadherin-3	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cell adhesion molecule binding cadherin binding protein binding beta-catenin binding	adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation positive regulation of keratinocyte proliferation positive regulation of epithelial cell proliferation regulation of keratinocyte proliferation biological regulation adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation positive regulation of keratinocyte proliferation positive regulation of epithelial cell proliferation regulation of keratinocyte proliferation biological regulation positive regulation of biological process regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of cellular process keratinocyte proliferation multicellular organismal process multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis retina homeostasis regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process pigment metabolic process regulation of melanin biosynthetic process pigment biosynthetic process melanin metabolic process secondary metabolic process positive regulation of secondary metabolite biosynthetic process secondary metabolite biosynthetic process positive regulation of melanin biosynthetic process regulation of secondary metabolite biosynthetic process regulation of secondary metabolic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process melanin biosynthetic process cell migration cell motility cell adhesion cell-cell adhesion cell-cell adhesion mediated by cadherin cellular component biogenesis cellular component assembly cell junction assembly cell-cell junction assembly molting cycle process molting cycle hair cycle hair cycle process cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of cell communication positive regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway positive regulation of response to stimulus positive regulation of insulin-like growth factor receptor signaling pathway regulation of insulin-like growth factor receptor signaling pathway insulin-like growth factor receptor signaling pathway positive regulation of signaling establishment of organelle localization regulation of localization cellular localization transport cellular pigmentation localization pigmentation organelle localization establishment of localization in cell melanosome transport positive regulation of melanosome transport vesicle localization regulation of transport establishment of melanosome localization establishment of vesicle localization regulation of melanosome transport pigment granule transport establishment of localization establishment of pigment granule localization positive regulation of transport pigment granule localization melanosome localization developmental process anatomical structure morphogenesis anatomical structure development cell morphogenesis epithelium development keratinization epidermal cell differentiation cellular developmental process epidermis development animal organ development tissue development epithelial cell differentiation skin development cell differentiation keratinocyte differentiation sensory perception of light stimulus system process sensory perception nervous system process visual perception homophilic cell-cell adhesion regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of Wnt signaling pathway calcium-dependent cell-cell adhesion regulation of developmental process regulation of hair cycle catagen hair cycle phase multicellular organism development regulation of timing of catagen skin epidermis development hair follicle development regulation of multicellular organismal process hair follicle maturation regulation of hair follicle maturation regulation of multicellular organismal development biological phase negative regulation of developmental process developmental maturation negative regulation of timing of catagen anatomical structure maturation negative regulation of hair follicle maturation regulation of hair follicle development negative regulation of hair follicle development negative regulation of multicellular organismal process	cellular anatomical structure cell junction cell periphery plasma membrane membrane protein-containing complex extrinsic component of plasma membrane catenin complex plasma membrane protein complex membrane protein complex extrinsic component of membrane intracellular anatomical structure cytoplasm cell-cell junction cellular anatomical structure cell junction cell periphery plasma membrane membrane protein-containing complex extrinsic component of plasma membrane catenin complex plasma membrane protein complex membrane protein complex extrinsic component of membrane intracellular anatomical structure cytoplasm cell-cell junction adherens junction anchoring junction

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P22223	ulcerative colitis congenital hypotrichosis with juvenile macular dystrophy EEM syndrome non-small cell lung carcinoma Ovarian Cysts pilocytic astrocytoma atopic eczema colorectal adenoma corpus luteum cyst cutaneous melanoma hypotrichosis lung adenocarcinoma malignant pancreatic neoplasm ovarian cancer pancreatic ductal adenocarcinoma ulcerative colitis congenital hypotrichosis with juvenile macular dystrophy EEM syndrome non-small cell lung carcinoma Ovarian Cysts pilocytic astrocytoma atopic eczema colorectal adenoma corpus luteum cyst cutaneous melanoma hypotrichosis lung adenocarcinoma malignant pancreatic neoplasm ovarian cancer pancreatic ductal adenocarcinoma psoriasis atypical teratoid rhabdoid tumor colorectal cancer Crohn disease intellectual disability malignant colon neoplasm medulloblastoma ovarian cyst pancreatic intraductal papillary-mucinous neoplasm systemic lupus erythematosus breast cancer cutaneous lupus erythematosus interstitial lung disease malignant mesothelioma

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.