4XNM | pdb_00004xnm

Antibody Influenza H5 Complex

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)
A [auth L]	d4xnml2	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 L]	d4xnml1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d4xnma2	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 A]	d4xnma1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4xnmh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d4xnmh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4xnmb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d4xnmb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
A [auth L]		e4xnmL1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TAXi_N	F:	ECOD (20:10:01)
C [auth A]		e4xnmA1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TAXi_N	F:	ECOD (20:10:01)
F [auth D]		e4xnmD1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TAXi_N	F:	ECOD (20:10:01)
E [auth C]		e4xnmC1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TAXi_N	F:	ECOD (20:10:01)
B [auth H]		e4xnmH1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TAXi_N	F:	ECOD (20:10:01)
B [auth H]		e4xnmH2	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)
D [auth B]		e4xnmB2	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: TAXi_N	F:	ECOD (20:10:01)
D [auth B]		e4xnmB3	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth D]	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)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth B]	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
A [auth L], C [auth A]	H5.3 Fab	L-LAMBDA	Homo sapiens (human)	IGLV3-101, IGLJ101, IGLC1*02	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202609-0)
B [auth H], D [auth B]	H5.3 Fab	VH-CH1	Homo sapiens (human)	IGHV4-402, IGHJ502, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L], C [auth A]	Light Chain	IGLV3	Lambda	hemagglutinin	SAbDab (2026-03-13)
B [auth H], D [auth B]	Heavy Chain	IGHV4	-	hemagglutinin	SAbDab (2026-03-13)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L], C [auth A]	H5.3 FAB Light Chain	-	-	-
E [auth C], F [auth D]	Hemagglutinin	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
B [auth H], D [auth B]	H5.3 FAB Heavy Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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