6E3H | pdb_00006e3h

Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin

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
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 H]	d6e3hh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d6e3hl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d6e3hl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6e3hb1	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	automated matches	automated matches	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
B	d6e3hb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
A	d6e3ha1	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
A	d6e3ha2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087930	3001616	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 H]		e6e3hH1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F:	ECOD (develop294)
C [auth L]		e6e3hL1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F:	ECOD (develop294)
B		e6e3hB1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F:	ECOD (develop294)
A		e6e3hA1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
A	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
A	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	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
D [auth H]	Fab S9-3-37	VH-CH1	Homo sapiens (human)	IGHV1-1801, IGHV1-1804, IGHJ601, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
C [auth L]	Fab S9-3-37	L-KAPPA	Homo sapiens (human)	IGKV2-2401, IGKJ201, IGKJ202, IGKC04	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth H]	Heavy Chain	IGHV1	-	hemagglutinin ha2 \| hemagglutinin ha1	SAbDab (2026-03-20)
C [auth L]	Light Chain	IGKV2	Kappa	hemagglutinin ha2 \| hemagglutinin ha1	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth H]	antibody S9-3-37 heavy chain	-	-	-
C [auth L]	antibody S9-3-37 light chain	-	-	-
B	Hemagglutinin HA2	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 import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular component organization or biogenesis virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host	virion component viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part virion membrane
A	Hemagglutinin HA1	identical protein binding protein binding binding host cell surface 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 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	virion component virion membrane viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR001364	Haemagglutinin, influenzavirus A/B	Family
B	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
B	IPR000149	Haemagglutinin, influenzavirus A	Family
B	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
A	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A	IPR000149	Haemagglutinin, influenzavirus A	Family
A	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.