4HKZ | pdb_00004hkz

Trastuzumab Fab complexed with Protein L and Protein A fragments

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
Thera-SAbDab Antibody 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 E]	d4hkze1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Immunoglobulin-binding domains	Immunoglobulin-binding domains	automated matches	(Finegoldia magna ) [TaxId: 1260 ],	SCOPe (2.08)
D [auth E]	d4hkze2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Finegoldia magna ) [TaxId: 1260 ],	SCOPe (2.08)
C [auth H]	d4hkzh1	All alpha proteins	immunoglobulin/albumin-binding domain-like	Bacterial immunoglobulin/albumin-binding domains	Immunoglobulin-binding protein A modules	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
C [auth H]	d4hkzh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
B	d4hkzb_	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	d4hkza2	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	d4hkza1	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)
D [auth E]	SCOP2B Superfamily	Immunoglobulin-binding domains-like	8085561	3000399	SCOP2B (2022-06-29)
C [auth H]	SCOP2 Family	Immunoglobulin-binding protein A modules	8098331	4000790	SCOP2 (2022-06-29)
C [auth H]	SCOP2 Superfamily	Bacterial immunoglobulin/albumin-binding domains	8098332	3001373	SCOP2 (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 E]		e4hkzE1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
C [auth H]		e4hkzH1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)
B	Sigma70_r2,Sigma70_ner	e4hkzB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)
A		e4hkzA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth E]	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
C [auth H]	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)
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	INN name	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202611-0)
A	INN name	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 (202611-0)

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 fragment	SAbDab (2026-03-27)
A	Light Chain	IGKV1	Kappa	immunoglobulin g-binding protein a \| protein l fragment	SAbDab (2026-03-27)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B	Nesfrotamig	ERBB2/CD340/HER2, TNFRSF9/CD137/4-1BB, CD3E, SIRPA	Therapeutic SAbDab (2026-03-27)
A	Cinrebafusp	ERBB2/CD340/HER2, TNFRSF9/CD137/4-1BB, SIRPA, CD3E	Therapeutic SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth E]	Protein L fragment	protein-containing complex binding binding immunoglobulin binding IgG binding	-	-
C [auth H]	Immunoglobulin G-binding protein A	protein-containing complex binding binding immunoglobulin binding IgG binding	-	-
B	Trastuzumab heavy chain	-	-	-
A	Trastuzumab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
D [auth E]	IPR020840	Extracellular matrix-binding protein ebh, GA module	Domain
D [auth E]	IPR003147	Protein L, Ig light chain-binding	Repeat
D [auth E]	IPR040912	Repeat of unknown function DUF5633	Repeat
D [auth E]	IPR002988	Protein G-related albumin-binding (GA) module	Domain
D [auth E]	IPR035152	GA-like domain	Domain
D [auth E]	IPR019931	LPXTG cell wall anchor motif	Conserved Site
C [auth H]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
C [auth H]	IPR005877	YSIRK Gram-positive signal peptide	Domain
C [auth H]	IPR036779	LysM domain superfamily	Homologous Superfamily
C [auth H]	IPR005038	Octapeptide repeat	Repeat
C [auth H]	IPR003132	Protein A, Ig-binding domain	Domain
C [auth H]	IPR018392	LysM domain	Domain
C [auth H]	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.