Annotations: 4KDM

Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
F	d4kdmf_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
D	d4kdmd_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
B	d4kdmb_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
E	d4kdme1	All beta proteins	Viral protein domain	Viral protein domain	Influenza hemagglutinin headpiece	Hemagglutinin	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
E	d4kdme2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
C	d4kdmc1	All beta proteins	Viral protein domain	Viral protein domain	Influenza hemagglutinin headpiece	Hemagglutinin	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
C	d4kdmc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
A	d4kdma1	All beta proteins	Viral protein domain	Viral protein domain	Influenza hemagglutinin headpiece	Hemagglutinin	(Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
A	d4kdma2	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)
F	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087922	3001616	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087922	3001616	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087922	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)
F	Med6	e4kdmF1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Med6	ECOD (v295)
D	Med6	e4kdmD1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Med6	ECOD (v295)
B		e4kdmB01	A: alpha arrays	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F:	ECOD (v295)
E	adh_short	e4kdmE1	A: alpha arrays	X: Alpha-beta plaits	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: adh_short	ECOD (v295)
C	adh_short	e4kdmC1	A: alpha arrays	X: Alpha-beta plaits	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: adh_short	ECOD (v295)
A	adh_short	e4kdmA1	A: alpha arrays	X: Alpha-beta plaits	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: adh_short	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
D	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
B	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
E	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
E	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
C	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
C	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	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
A, C, E	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

InterPro: Protein Family Classification InterPro Database Homepage

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

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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.