6BAH

Trastuzumab Fab v3 with 5-diphenyl meditope variant

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Immunoglobulin-binding domains-like	8085561	3000399	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_4	e6bahA2	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	e6bahA1	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	e6bahB2	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	e6bahB1	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 E]	B1	e6bahE1	A: a+b two layers	X: beta-Grasp	H: Immunoglobulin-binding domains (From Topology)	T: Immunoglobulin-binding domains	F: B1	ECOD (1.6)
D [auth C]	B	e6bahC1	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)

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 (utative)
C [auth E]	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Light Chain	IGKV1	Kappa	immunoglobulin g binding protein a \| protein l	SAbDab (2024-04-12)
B	Heavy Chain	IGHV3	-	immunoglobulin g binding protein a \| protein l	SAbDab (2024-04-12)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	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
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 ...	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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Trastuzumab Fab light chain,Immunoglobulin kappa constant	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
B	Trastuzumab Fab heavy chain,IGH@ protein	-	-	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex
C [auth E]	Protein L	protein-containing complex binding binding immunoglobulin binding IgG binding	-	-
D [auth C]	Immunoglobulin G binding protein A	protein-containing complex binding binding immunoglobulin binding IgG binding	-	extracellular region cellular anatomical entity
E [auth D]	meditope	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
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
B	IPR003597	Immunoglobulin C1-set	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR003599	Immunoglobulin subtype	Domain
B	IPR013106	Immunoglobulin V-set domain	Domain
B	IPR007110	Immunoglobulin-like domain	Domain
B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
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
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

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth D]	2GX	Parent Component: PHE
E [auth D]	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359