6K68 | pdb_00006k68

Application of anti-helix antibodies in protein structure determination (8420-3MNZ)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	ubiquitin	e6k68L1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
I	ubiquitin	e6k68I1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
H	ubiquitin	e6k68H1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
E	Oxidored_nitro,DUF3364	e6k68E1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Oxidored_nitro,DUF3364	ECOD (v294.1)
K	ubiquitin	e6k68K1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
G	ubiquitin	e6k68G1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
D	ubiquitin	e6k68D1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
B	Oxidored_nitro,DUF3364	e6k68B1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Oxidored_nitro,DUF3364	ECOD (v294.1)
J	Oxidored_nitro,DUF3364	e6k68J1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Oxidored_nitro,DUF3364	ECOD (v294.1)
F	ubiquitin	e6k68F1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
C	ubiquitin	e6k68C1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
A	ubiquitin	e6k68A1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	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 (utative)
I	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 (utative)
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 (utative)
E	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 (utative)

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
E, H, I, L	SpA IgG-binding domain proteinA	SPA	Homo sapiens (human)	SpA*01	R-LIKE-DOMAIN SPA-DOMAIN	RPI	Protein	IMGT (202611-0)
B, D, G, K	Fv 8420-3MNZ	V-KAPPA	Homo sapiens (human)	IGKV8-2401, IGKJ101	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202611-0)
A, C, F, J	Fv 8420-3MNZ	VH	Homo sapiens (human)	IGHV9-2-101, IGHJ201	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D, G, K	Light Chain	IGKV8	Kappa	protein a	SAbDab (2026-03-27)
A, C, F, J	Heavy Chain	IGHV9	-	protein a	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, H, I, L	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
B, D, G, K	3MNZ Variable light chain	-	-	-
A, C, F, J	3MNZ Variable heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, H, I, L	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
E, H, I, L	IPR005877	YSIRK Gram-positive signal peptide	Domain
E, H, I, L	IPR036779	LysM domain superfamily	Homologous Superfamily
E, H, I, L	IPR005038	Octapeptide repeat	Repeat
E, H, I, L	IPR003132	Protein A, Ig-binding domain	Domain
E, H, I, L	IPR018392	LysM domain	Domain
E, H, I, L	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.