5T6S

Crystal structure of the A/Shanghai/2/2013 (H7N9) influenza virus hemagglutinin in complex with the antiviral drug arbidol

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5t6sa_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
C	d5t6sc_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
E	d5t6se_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
G	d5t6sg_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
I	d5t6si_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
K	d5t6sk_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
B	d5t6sb_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
D	d5t6sd_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
F	d5t6sf_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
H	d5t6sh_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
J	d5t6sj_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	SCOPe (2.08)
L	d5t6sl_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	automated matches	automated matches	(Influenza A virus (A/Shanghai/02/2013(H7N9)) ) [TaxId: 1332244 ],	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	8087858	3001342	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087858	3001342	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087858	3001342	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087858	3001342	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087858	3001342	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087858	3001342	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088020	3001616	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088020	3001616	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088020	3001616	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088020	3001616	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088020	3001616	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088020	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	e5t6sA1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
C	Hemagglutinin_1st	e5t6sC1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
E	Hemagglutinin_1st	e5t6sE1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
G	Hemagglutinin_1st	e5t6sG1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
I	Hemagglutinin_1st	e5t6sI1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
K	Hemagglutinin_1st	e5t6sK1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
B	Hemagglutinin_2nd	e5t6sB1	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)
D	Hemagglutinin_2nd	e5t6sD1	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	e5t6sF1	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)
H	Hemagglutinin_2nd	e5t6sH1	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)
J	Hemagglutinin_2nd	e5t6sJ1	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)
L	Hemagglutinin_2nd	e5t6sL1	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 (4.3.0)
A	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)
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)
G	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
G	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
I	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
I	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
K	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
K	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
B	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)
F	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
H	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
J	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
L	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family
B, D, F, H, J B, D, F, H, J, L	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	Hemagglutinin HA1	cation binding ion binding binding metal ion binding small molecule 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 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 transport of virus	virion component virion membrane cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part virion component virion membrane cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane
B, D, F, H, J B, D, F, H, J, L	Hemagglutinin HA2	cation binding ion binding binding metal ion binding small molecule 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 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 transport of virus	virion component virion membrane cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part virion component virion membrane cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane

InterPro: Protein Family Classification InterPro Database Homepage

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