5VEB

Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6

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	d5veba_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5vebb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5vebb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d5vebl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d5vebl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d5vebh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ], (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)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	SCOP2B (2022-06-29)
D [auth L]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	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	C1-set_1	e5vebA2	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)
A	V-set_12	e5vebA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
B	C1-set_4	e5vebB2	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	V-set	e5vebB1	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)
D [auth L]	C1-set_4	e5vebL1	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)
D [auth L]	V-set	e5vebL2	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 [auth H]	C1-set_1	e5vebH1	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)
C [auth H]	V-set_12	e5vebH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
E [auth X]	Cadherin_1	e5vebX1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Cadherin_1	ECOD (1.6)
F [auth Y]	Cadherin_1	e5vebY1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Cadherin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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	Antibody Fab Fragment, anti-CDH6	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHV3-3003, IGHV3-3006, IGHV3-3012, IGHV3-3019, IGHV3-3305, IGHV3-NL101, IGHV3-23D01, IGHJ501, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B, D [auth L]	Antibody Fab Fragment, anti-CDH6	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
C [auth H]	Antibody Fab Fragment, anti-CDH6	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHV3-3003, IGHV3-3006, IGHV3-3012, IGHV3-3019, IGHV3-3305, IGHV3-NL101, IGHV3-23D01, IGHJ501, IGHG103	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
A	Heavy Chain	IGHV3	-	cadherin-6	SAbDab (2024-04-19)
B, D [auth L]	Light Chain	IGKV1	Kappa	cadherin-6	SAbDab (2024-04-19)
C [auth H]	Heavy Chain	IGHV3	-	cadherin-6	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B, D [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
C [auth H]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
E [auth X], F [auth Y]	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	anti-CDH6 Fab heavy chain	-	-	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex
B, D [auth L]	anti-CDH6 Fab light chain	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response	protein-containing complex IgA immunoglobulin complex immunoglobulin complex extracellular region extracellular space cellular anatomical entity blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle protein-containing complex IgA immunoglobulin complex immunoglobulin complex extracellular region extracellular space cellular anatomical entity blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex
C [auth H]	anti-CDH6 Fab heavy chain	-	-	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex
E [auth X], F [auth Y]	Cadherin-6	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cell adhesion molecule binding cadherin binding protein binding	adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization developmental process anatomical structure morphogenesis anatomical structure development cell morphogenesis cell adhesion cell-cell adhesion synaptic membrane adhesion synapse organization adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization developmental process anatomical structure morphogenesis anatomical structure development cell morphogenesis cell adhesion cell-cell adhesion synaptic membrane adhesion synapse organization cell-cell adhesion via plasma-membrane adhesion molecules homophilic cell adhesion via plasma membrane adhesion molecules cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication Notch signaling pathway signal transduction calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules cell-cell adhesion mediated by cadherin cellular component biogenesis cellular component assembly cell junction assembly cell-cell junction assembly	cell-cell junction adherens junction anchoring junction cell junction cellular anatomical entity 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 cell-cell junction adherens junction anchoring junction cell junction cellular anatomical entity 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 membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen synapse glutamatergic synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003597	Immunoglobulin C1-set	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR003599	Immunoglobulin subtype	Domain
A	IPR013106	Immunoglobulin V-set domain	Domain
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B, D [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, D [auth L]	IPR003597	Immunoglobulin C1-set	Domain
B, D [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D [auth L]	IPR007110	Immunoglobulin-like domain	Domain
B, D [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth H]	IPR003597	Immunoglobulin C1-set	Domain
C [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H]	IPR003599	Immunoglobulin subtype	Domain
C [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth H]	IPR007110	Immunoglobulin-like domain	Domain
C [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
E [auth X], F [auth Y]	IPR000233	Cadherin, Y-type LIR-motif	Domain
E [auth X], F [auth Y]	IPR027397	Catenin binding domain superfamily	Homologous Superfamily
E [auth X], F [auth Y]	IPR039808	Cadherin	Family
E [auth X], F [auth Y]	IPR015919	Cadherin-like superfamily	Homologous Superfamily
E [auth X], F [auth Y]	IPR020894	Cadherin conserved site	Conserved Site
E [auth X], F [auth Y]	IPR002126	Cadherin-like	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D [auth L]	Pharos: P01834	recurrent infections associated with rare immunoglobulin isotypes deficiency myositis dysgammaglobulinemia Hepatomegaly acquired idiopathic inflammatory myopathy selective IgG immunodeficiency
E [auth X], F [auth Y]	Pharos: P55285	Cachexia non-alcoholic fatty liver disease ovarian cancer interstitial cystitis oligodendroglioma transitional cell carcinoma malignant ependymoma osteosarcoma