5WKO

Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1) influenza virus

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
M	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	SCOP2B (2022-06-29)
P	SCOP2 Family	Influenza hemagglutinin (stalk)	8097431	4003840	SCOP2 (2022-06-29)
P	SCOP2 Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2 (2022-06-29)
Q	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2B (2022-06-29)
X	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	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	PF07654	e5wkoA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A	PF07686	e5wkoA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C	PF07654	e5wkoC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C	PF07686	e5wkoC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E	PF07654	e5wkoE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E	PF07686	e5wkoE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
G	PF07654	e5wkoG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
G	PF07686	e5wkoG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I	PF07654	e5wkoI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
I	PF07686	e5wkoI2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
K	PF07654	e5wkoK2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
K	PF07686	e5wkoK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B	PF07654	e5wkoB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B	PF07686	e5wkoB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07654	e5wkoD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D	PF07686	e5wkoD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F	PF07654	e5wkoF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
F	PF07686	e5wkoF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H	PF07654	e5wkoH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
H	PF07686	e5wkoH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J	PF07654	e5wkoJ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
J	PF07686	e5wkoJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
L	PF07654	e5wkoL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
L	PF07686	e5wkoL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
M	PF00509	e5wkoM1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
N	PF00509	e5wkoN1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
O	PF00509	e5wkoO1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
S	PF00509	e5wkoS1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
T	PF00509	e5wkoT1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
U	PF00509	e5wkoU1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
P	PF00509	e5wkoP1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: PF00509	ECOD (1.6)
Q	PF00509	e5wkoQ1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: PF00509	ECOD (1.6)
R	PF00509	e5wkoR1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: PF00509	ECOD (1.6)
V	PF00509	e5wkoV1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: PF00509	ECOD (1.6)
W	PF00509	e5wkoW1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: PF00509	ECOD (1.6)
X	PF00509	e5wkoX1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: PF00509	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
M	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
M	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
N	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
N	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
O	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
O	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
S	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
S	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
T	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
T	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
U	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
U	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	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, C, E, G, I A, C, E, G, I, K	Fab 27F3, broadly neutralizing	VH-CH1	Homo sapiens (human)	IGHV1-6901, IGHV1-6906, IGHV1-6912, IGHV1-6913, IGHV1-6914, IGHV1-69D01, IGHJ603, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
B, D, F, H, J B, D, F, H, J, L	Fab 27F3, broadly neutralizing	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C, E, G, I A, C, E, G, I, K	Heavy Chain	IGHV1	-	hemagglutinin \| hemagglutinin	SAbDab (2024-04-26)
B, D, F, H, J B, D, F, H, J, L	Light Chain	IGKV3	Kappa	hemagglutinin \| hemagglutinin	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A, C, E, G, I A, C, E, G, I, K	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B, D, F, H, J B, D, F, H, J, L	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B, D, F, H, J B, D, F, H, J, L	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
M, N, O, S, T M, N, O, S, T, U	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family
P, Q, R, V, W P, Q, R, V, W, X	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	Antibody 27F3 heavy chain	-	-	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex
B, D, F, H, J B, D, F, H, J, L	Antibody 27F3 light chain	-	-	extracellular region cellular anatomical entity
M, N, O, S, T M, N, O, S, T, U	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 transport of virus	virion component virion membrane cell periphery apical part of cell membrane plasma membrane plasma membrane region cellular anatomical entity apical plasma membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part virion component virion membrane cell periphery apical part of cell membrane plasma membrane plasma membrane region cellular anatomical entity apical plasma membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane
P, Q, R, V, W P, Q, R, V, W, X	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 transport of virus	virion component virion membrane cell periphery apical part of cell membrane plasma membrane plasma membrane region cellular anatomical entity apical plasma membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part virion component virion membrane cell periphery apical part of cell membrane plasma membrane plasma membrane region cellular anatomical entity 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	IPR003597	Immunoglobulin C1-set	Domain
A, C, E, G, I A, C, E, G, I, K	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR003599	Immunoglobulin subtype	Domain
A, C, E, G, I A, C, E, G, I, K	IPR013106	Immunoglobulin V-set domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR007110	Immunoglobulin-like domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B, D, F, H, J B, D, F, H, J, L	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR003599	Immunoglobulin subtype	Domain
B, D, F, H, J B, D, F, H, J, L	IPR013106	Immunoglobulin V-set domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR007110	Immunoglobulin-like domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR003597	Immunoglobulin C1-set	Domain
B, D, F, H, J B, D, F, H, J, L	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR003599	Immunoglobulin subtype	Domain
B, D, F, H, J B, D, F, H, J, L	IPR013106	Immunoglobulin V-set domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR007110	Immunoglobulin-like domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
M, N, O, S, T M, N, O, S, T, U	IPR001364	Haemagglutinin, influenzavirus A/B	Family
M, N, O, S, T M, N, O, S, T, U	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
M, N, O, S, T M, N, O, S, T, U	IPR000149	Haemagglutinin, influenzavirus A	Family
M, N, O, S, T M, N, O, S, T, U	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
P, Q, R, V, W P, Q, R, V, W, X	IPR001364	Haemagglutinin, influenzavirus A/B	Family
P, Q, R, V, W P, Q, R, V, W, X	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
P, Q, R, V, W P, Q, R, V, W, X	IPR000149	Haemagglutinin, influenzavirus A	Family
P, Q, R, V, W P, Q, R, V, W, X	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily