6VMZ

Crystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6vmza1	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/chicken/Vietnam/4/2003(H5N1)) ) [TaxId: 380835 ],	SCOPe (2.08)
A	d6vmza2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Influenza A virus (A/chicken/Vietnam/4/2003(H5N1)) ) [TaxId: 380835 ],	SCOPe (2.08)
B [auth C]	d6vmzc1	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/chicken/Vietnam/4/2003(H5N1)) ) [TaxId: 380835 ],	SCOPe (2.08)
B [auth C]	d6vmzc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Influenza A virus (A/chicken/Vietnam/4/2003(H5N1)) ) [TaxId: 380835 ],	SCOPe (2.08)
C [auth E]	d6vmze1	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/chicken/Vietnam/4/2003(H5N1)) ) [TaxId: 380835 ],	SCOPe (2.08)
C [auth E]	d6vmze2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Influenza A virus (A/chicken/Vietnam/4/2003(H5N1)) ) [TaxId: 380835 ],	SCOPe (2.08)
D [auth B]	d6vmzb_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	(Influenza A virus (A/chicken/Vietnam/30/2003(H5N1)) ) [TaxId: 380830 ],	SCOPe (2.08)
E [auth D]	d6vmzd_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	(Influenza A virus (A/chicken/Vietnam/30/2003(H5N1)) ) [TaxId: 380830 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087758	3001342	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087758	3001342	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087758	3001342	SCOP2B (2022-06-29)
D [auth B]	SCOP2 Family	Influenza hemagglutinin (stalk)	8099217	4003840	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	Influenza hemagglutinin (stalk)	8099218	3001616	SCOP2 (2022-06-29)
E [auth D]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8099218	3001616	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8099218	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)
A	Hemagglutinin_1st	e6vmzA1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
B [auth C]	Hemagglutinin_1st	e6vmzC1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
C [auth E]	Hemagglutinin_1st	e6vmzE1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
D [auth B]	Hemagglutinin_2nd	e6vmzB1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: Hemagglutinin_2nd	ECOD (1.6)
E [auth D]	Hemagglutinin_2nd	e6vmzD1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: Hemagglutinin_2nd	ECOD (1.6)
F	Hemagglutinin_2nd	e6vmzF1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: Hemagglutinin_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family
D [auth B], E [auth D], F	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth E]	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 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 transport of virus 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 host cell part host cell membrane cellular anatomical entity cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane
D [auth B], E [auth D], 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 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 transport of virus 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 host cell part host cell membrane cellular anatomical entity cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.