6N5D | pdb_00006n5d

Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope

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)
I [auth D]	d6n5dd2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
I [auth D]	d6n5dd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth F]	d6n5df2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth F]	d6n5df1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth N]	d6n5dn2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth N]	d6n5dn1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth L]	d6n5dl_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth E]	d6n5de_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth C]	d6n5dc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth K]	d6n5dk_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus ) [TaxId: 11320 ],	SCOPe (2.08)
C [auth B]	d6n5db_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus ) [TaxId: 11320 ],	SCOPe (2.08)
A	d6n5da_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus ) [TaxId: 11320 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth K]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087826	3001342	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087826	3001342	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087826	3001342	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)
I [auth D]	Sigma70_r2,Sigma70_ner	e6n5dD1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)
H [auth F]	Sigma70_r2,Sigma70_ner	e6n5dF1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)
G [auth N]		e6n5dN1	A: alpha bundles	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F:	ECOD (develop294)
F [auth L]	Sigma70_r2,Sigma70_ner	e6n5dL1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)
D [auth E]	Sigma70_r2,Sigma70_ner	e6n5dE1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)
B [auth C]	Sigma70_r2,Sigma70_ner	e6n5dC1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)
E [auth K]	Sigma70_r2,Sigma70_ner	e6n5dK1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)
C [auth B]	Sigma70_r2,Sigma70_ner	e6n5dB1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (develop294)
A		e6n5dA1	A: alpha bundles	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
H [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
G [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth K]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (utative)
E [auth K]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (utative)
C [auth B]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (utative)
C [auth B]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (utative)
A	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (utative)
A	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	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
G [auth N], H [auth F], I [auth D]	Antibody Fab Fragment, broadly neutralizing antibody	L-LAMBDA	Mus musculus (house mouse)	IGLV101, IGLJ101, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
B [auth C], D [auth E], F [auth L]	Antibody Fab Fragment, broadly neutralizing antibody	VH-CH1	Mus musculus (house mouse)	IGHV5-9-102, IGHJ301, IGHG103, IGHG108, IGHG1*06	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth N], H [auth F], I [auth D]	Light Chain	IGLV1	Lambda	hemagglutinin	SAbDab (2026-03-20)
B [auth C], D [auth E], F [auth L]	Heavy Chain	IGHV5	-	hemagglutinin	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth K]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth N], H [auth F], I [auth D]	antibody light chain	-	-	-
B [auth C], D [auth E], F [auth L]	antibody heavy chain	-	-	-
A, C [auth B], E [auth K]	Hemagglutinin	host cell surface binding binding host cell surface receptor binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction non-lytic viral release viral budding virion assembly exit from host cell viral budding from plasma membrane viral release from host cell import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell	cellular anatomical structure membrane virion component virion membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth K]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A, C [auth B], E [auth K]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A, C [auth B], E [auth K]	IPR000149	Haemagglutinin, influenzavirus A	Family
A, C [auth B], E [auth K]	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily

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.