6B9Z | pdb_00006b9z

Trastuzumab Fab v3

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth C]	d6b9zc1	All alpha proteins	immunoglobulin/albumin-binding domain-like	Bacterial immunoglobulin/albumin-binding domains	Immunoglobulin-binding protein A modules	Immunoglobulin-binding protein A modules	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
D [auth C]	d6b9zc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C [auth E]	d6b9ze1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Immunoglobulin-binding domains	Immunoglobulin-binding domains	automated matches	Peptostreptococcus magnus (Finegoldia magna ) [TaxId: 1260 ],	SCOPe (2.08)
C [auth E]	d6b9ze2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Peptostreptococcus magnus (Finegoldia magna ) [TaxId: 1260 ],	SCOPe (2.08)
B	d6b9zb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6b9za2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	(Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6b9za1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ], 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 [auth E]	SCOP2B Superfamily	Immunoglobulin-binding domains-like	8085561	3000399	SCOP2B (2022-06-29)
A	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)
D [auth C]	B	e6b9zC1	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Bacterial immunoglobulin/albumin-binding domains (From Topology)	T: Bacterial immunoglobulin/albumin-binding domains	F: B	ECOD (1.6)
C [auth E]	B1	e6b9zE1	A: a+b two layers	X: beta-Grasp	H: Immunoglobulin-binding domains (From Topology)	T: Immunoglobulin-binding domains	F: B1	ECOD (1.6)
B	V-set_8	e6b9zB1	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	C1-set_1	e6b9zB2	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	C1-set_4	e6b9zA2	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)
A	V-set	e6b9zA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	1.20.5.420	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Immunoglobulin FC, subunit C	CATH (4.3.0)
C [auth E]	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV3	-	immunoglobulin g binding protein a \| protein l	SAbDab (2025-12-19)
A	Light Chain	IGKV1	Kappa	immunoglobulin g binding protein a \| protein l	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth C]	PF02216	B domain (B)	B domain	This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.	Domain
C [auth E]	PF02246	Protein L b1 domain (B1)	Protein L b1 domain	Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig l ...	Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig light chains [1].	Domain
B	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
B	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth C]	Immunoglobulin G binding protein A	protein-containing complex binding binding immunoglobulin binding IgG binding	symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host signal transduction pathway via antagonism of host cell surface receptor symbiont-mediated perturbation of host process symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction	cellular anatomical structure extracellular region
C [auth E]	Protein L	protein-containing complex binding binding immunoglobulin binding IgG binding	-	cellular anatomical structure extracellular region
B	Trastuzumab Fab heavy chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
A	Trastuzumab 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 cellular anatomical structure extracellular region extracellular space 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 cellular anatomical structure extracellular region extracellular space 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth C]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
D [auth C]	IPR005877	YSIRK Gram-positive signal peptide	Domain
D [auth C]	IPR036779	LysM domain superfamily	Homologous Superfamily
D [auth C]	IPR005038	Octapeptide repeat	Repeat
D [auth C]	IPR003132	Protein A, Ig-binding domain	Domain
D [auth C]	IPR018392	LysM domain	Domain
D [auth C]	IPR019931	LPXTG cell wall anchor domain	Domain
C [auth E]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
C [auth E]	IPR020840	Extracellular matrix-binding protein ebh, GA module	Domain
C [auth E]	IPR003147	Protein L, Ig light chain-binding	Repeat
C [auth E]	IPR040912	Repeat of unknown function DUF5633	Repeat
C [auth E]	IPR002988	Protein G-related albumin-binding (GA) module	Domain
C [auth E]	IPR035152	GA-like domain	Domain
C [auth E]	IPR019931	LPXTG cell wall anchor domain	Domain
B	IPR003597	Immunoglobulin C1-set	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR013106	Immunoglobulin V-set domain	Domain
B	IPR003599	Immunoglobulin domain subtype	Domain
B	IPR007110	Immunoglobulin-like domain	Domain
B	IPR050380	Immune Recognition and Response Modulators	Family
B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR050380	Immune Recognition and Response Modulators	Family
A	IPR003597	Immunoglobulin C1-set	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P01834	recurrent infections associated with rare immunoglobulin isotypes deficiency myositis dysgammaglobulinemia Hepatomegaly acquired idiopathic inflammatory myopathy selective IgG immunodeficiency