Annotations: 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
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)
X	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8097432	3001616	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)
U	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)
S	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)
N	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	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)
X	Peptidase_S26	e5wkoX1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
W	Peptidase_S26	e5wkoW1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
V	Peptidase_S26	e5wkoV1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
R	Peptidase_S26	e5wkoR1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
Q	Peptidase_S26	e5wkoQ1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
P	Peptidase_S26	e5wkoP1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
U	Peptidase_S26	e5wkoU1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
T	Peptidase_S26	e5wkoT1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
S	Peptidase_S26	e5wkoS1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
O	Peptidase_S26	e5wkoO1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
N	Peptidase_S26	e5wkoN1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
M	Peptidase_S26	e5wkoM1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
L	Peptidase_S26	e5wkoL1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
J	Peptidase_S26	e5wkoJ1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
H	Peptidase_S26	e5wkoH1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
F	Peptidase_S26	e5wkoF1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
D	Peptidase_S26	e5wkoD1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
B	Peptidase_S26	e5wkoB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
K	Peptidase_S26	e5wkoK1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
I	Peptidase_S26	e5wkoI1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
G	Peptidase_S26	e5wkoG1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
E	Peptidase_S26	e5wkoE1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
C	Peptidase_S26	e5wkoC1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)
A	Peptidase_S26	e5wkoA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
X	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)
W	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)
V	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)
R	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)
Q	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)
P	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)
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)
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)
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)
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)
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)
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)
L	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)
H	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)
D	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)
K	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)
G	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)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	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
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 (202615-0)
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 (202615-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D, F, H, J B, D, F, H, J, L	Light Chain	IGKV3	Kappa	hemagglutinin \| hemagglutinin	SAbDab (2026-04-24)
A, C, E, G, I A, C, E, G, I, K	Heavy Chain	IGHV1	-	hemagglutinin \| hemagglutinin	SAbDab (2026-04-24)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	cellular anatomical structure membrane virion component virion membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane other organism part
M, N, O, S, T M, N, O, S, T, U	Hemagglutinin	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	cellular anatomical structure membrane virion component virion membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane other organism part
B, D, F, H, J B, D, F, H, J, L	Antibody 27F3 light chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
A, C, E, G, I A, C, E, G, I, K	Antibody 27F3 heavy chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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
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	IPR050150	Immunoglobulin Variable Light Chain	Family
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	IPR013106	Immunoglobulin V-set domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR003599	Immunoglobulin domain subtype	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
B, D, F, H, J B, D, F, H, J, L	IPR050150	Immunoglobulin Variable Light Chain	Family
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	IPR013106	Immunoglobulin V-set domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR003599	Immunoglobulin domain subtype	Domain
B, D, F, H, J B, D, F, H, J, L	IPR007110	Immunoglobulin-like domain	Domain
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	IPR013106	Immunoglobulin V-set domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR003599	Immunoglobulin domain subtype	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	IPR050380	Immune Recognition and Response Modulators	Family
A, C, E, G, I A, C, E, G, I, K	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site