4YK4 | pdb_00004yk4

Human antibody 641 I-9 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B [auth Z]	d4yk4z1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth Z]	d4yk4z2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d4yk4c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d4yk4c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4yk4b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4yk4b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth Y]	d4yk4y2	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 [auth Y]	d4yk4y1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth Z]		e4yk4Z2	A: TBP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: SNase	F:	ECOD (20:10:01)
B [auth Z]		e4yk4Z3	A: Lipocalins/Streptavidin	X: SAM/DNA-glycosylase	H: SAM domain-like	T: EF-hand_1, EF-hand_6, EF-hand_7	F:	ECOD (20:10:01)
E [auth C]		e4yk4C2	A: TBP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: SNase	F:	ECOD (20:10:01)
E [auth C]		e4yk4C3	A: Lipocalins/Streptavidin	X: SAM/DNA-glycosylase	H: SAM domain-like	T: EF-hand_1, EF-hand_6, EF-hand_7	F:	ECOD (20:10:01)
F [auth A]		e4yk4A1	A: TBP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: SNase	F:	ECOD (20:10:01)
C [auth E]		e4yk4E1	A: TBP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: SNase	F:	ECOD (20:10:01)
D [auth B]		e4yk4B1	A: TBP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: SNase	F:	ECOD (20:10:01)
A [auth Y]		e4yk4Y1	A: TBP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: SNase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth Z]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth A]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
C [auth E]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
D [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth Y]	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 [auth Z], E [auth C]	641 I-9 Fab	VH-CH1	Homo sapiens (human)	IGHV4-5901, IGHV4-5903, IGHV4-5908, IGHJ603, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)
A [auth Y], D [auth B]	641 I-9 Fab	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ501, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	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
B [auth Z], E [auth C]	Heavy Chain	IGHV4	-	hemagglutinin	SAbDab (2026-03-13)
A [auth Y], D [auth B]	Light Chain	IGKV1	Kappa	hemagglutinin	SAbDab (2026-03-13)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth Z], E [auth C]	641 I-9 VHCH antibody	-	-	-
C [auth E], F [auth A]	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 [auth Y], D [auth B]	641 I-9 VLCL antibody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E], F [auth A]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
C [auth E], F [auth A]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
C [auth E], F [auth A]	IPR000149	Haemagglutinin, influenzavirus A	Family
C [auth E], F [auth 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.