5U3D | pdb_00005u3d

STRUCTURE OF MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth C]	d5u3dc1	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]	d5u3dc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C [auth E]	d5u3de1	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]	d5u3de2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Peptostreptococcus magnus (Finegoldia magna ) [TaxId: 1260 ],	SCOPe (2.08)
B	d5u3db_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5u3da2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5u3da1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth C]		e5u3dC1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: Peptidase_M42	F:	ECOD (20:10:01)
C [auth E]		e5u3dE1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: Peptidase_M42	F:	ECOD (20:10:01)
B		e5u3dB1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: F_bP_aldolase	F:	ECOD (20:10:01)
A		e5u3dA1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: Peptidase_M42	F:	ECOD (20:10:01)

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 (4.3.0)
A	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
B	Fab Memab trastuzumab	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)
A	Fab Memab trastuzumab	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV3	-	protein l	SAbDab (2026-03-13)
A	Light Chain	IGKV1	Kappa	protein l	SAbDab (2026-03-13)

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

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	-	-
B	MEMAB TRASTUZUMAB FAB HEAVY CHAIN	-	-	-
A	MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E	-	-	-

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 motif	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 motif	Conserved Site

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.