6DN0 | pdb_00006dn0

Retrofitted antibodies with stabilizing mutations: Herceptin scFv mutant with VH K30D and VL S52D.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6dn0d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6dn0b_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6dn0c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6dn0a_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6dn0D1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
B	DAO	e6dn0B1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (develop294)
C	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6dn0C1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
A	DAO	e6dn0A1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DAO	ECOD (develop294)

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, D	Fv Herceptin mutant VH K30D and VL S52D	V-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ1*01	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202610-0)
A, C	Fv Herceptin mutant VH K30D and VL S52D	VH	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ101	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Light Chain	IGKV1	Kappa	-	SAbDab (2026-03-20)
A, C	Heavy Chain	IGHV3	-	-	SAbDab (2026-03-20)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B, D	Caxmotabart	ERBB2/CD340/HER2, TNFRSF9/CD137/4-1BB, SIRPA, CD3E	Therapeutic SAbDab (2026-03-20)
A, C	Trastuzumab	ERBB2/CD340/HER2, TNFRSF9/CD137/4-1BB, SIRPA, CD3E	Therapeutic SAbDab (2026-03-20)

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.