5Y2M | pdb_00005y2m

Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the H4N6 duck isolate (H4-CZ/56) hemagglutinin

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Influenza hemagglutinin headpiece	8097077	4002506	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Influenza hemagglutinin domain-like	8097078	3001342	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8097078	3001342	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8097078	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)
H [auth J]		e5y2mJ1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: PDZ_6	F:	ECOD (20:10:01)
J [auth L]		e5y2mL1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: Actin	F:	ECOD (20:10:01)
G [auth I]		e5y2mI1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: PDZ_6	F:	ECOD (20:10:01)
I [auth K]		e5y2mK1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: Actin	F:	ECOD (20:10:01)
B [auth D]		e5y2mD1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: PDZ_6	F:	ECOD (20:10:01)
D [auth E]		e5y2mE1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: Actin	F:	ECOD (20:10:01)
F		e5y2mF1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: Actin	F:	ECOD (20:10:01)
A		e5y2mA1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: PDZ_6	F:	ECOD (20:10:01)
C [auth B]		e5y2mB1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: Actin	F:	ECOD (20:10:01)
E [auth C]		e5y2mC1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: Actin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
I [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth D]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
D [auth E]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
F	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
A	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
C [auth B]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
E [auth C]	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
H [auth J], J [auth L]	Fab AF4H1K1	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ101, IGKJ1S201, IGKJ301, IGKJ401, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)
G [auth I], I [auth K]	Fab AF4H1K1	VH-CH1	Homo sapiens (human)	IGHV3-3001, IGHV3-3004, IGHV3-3007, IGHV3-3011, IGHV3-3014, IGHV3-3016, IGHV3-3017, IGHV3-30-301, IGHV3-30-303, IGHJ401, IGHJ402, IGHJ403, IGHG103, IGHG108, IGHG1*06	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
H [auth J], J [auth L]	Light Chain	IGKV3	Kappa	hemagglutinin \| hemagglutinin \| hemagglutinin, hemagglutinin \| hemagglutinin	SAbDab (2026-03-13)
G [auth I], I [auth K]	Heavy Chain	IGHV3	-	hemagglutinin \| hemagglutinin \| hemagglutinin, hemagglutinin \| hemagglutinin	SAbDab (2026-03-13)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth J], J [auth L]	a group 2 HA binding antibody AF4H1K1 Fab light chain	-	-	-
G [auth I], I [auth K]	a group 2 HA binding antibody AF4H1K1 Fab heavy chain	-	-	-
B [auth D], D [auth E], F	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
A, C [auth B], E [auth C]	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
B [auth D], D [auth E], F	IPR001364	Haemagglutinin, influenzavirus A/B	Family
B [auth D], D [auth E], F	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
B [auth D], D [auth E], F	IPR000149	Haemagglutinin, influenzavirus A	Family
B [auth D], D [auth E], F	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A, C [auth B], E [auth C]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A, C [auth B], E [auth C]	IPR000149	Haemagglutinin, influenzavirus A	Family
A, C [auth B], E [auth C]	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.