6B3M | pdb_00006b3m

The crystal structure of a broadly-reactive human anti-hemagglutinin stalk antibody (70-1F02) in complex with H5 hemagglutinin

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)
E [auth F]	SCOP2 Family	Influenza hemagglutinin (stalk)	8087909	4003840	SCOP2 (2022-06-29)
E [auth F]	SCOP2 Superfamily	Influenza hemagglutinin (stalk)	8087910	3001616	SCOP2 (2022-06-29)
G [auth H]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087910	3001616	SCOP2B (2022-06-29)
Q [auth T]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087910	3001616	SCOP2B (2022-06-29)
O [auth R]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087910	3001616	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087910	3001616	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087910	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)
X [auth N]	C1-set_4	e6b3mN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
X [auth N]	V-set	e6b3mN2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
W	C1-set_4	e6b3mW1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
W	V-set	e6b3mW2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
V [auth D]	C1-set_4	e6b3mD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
V [auth D]	V-set	e6b3mD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
U [auth J]	C1-set_4	e6b3mJ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
U [auth J]	V-set	e6b3mJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
T [auth U]	C1-set_4	e6b3mU1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
T [auth U]	V-set	e6b3mU2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
M [auth P]	C1-set_4	e6b3mP2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
M [auth P]	V-set	e6b3mP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
S [auth Y]	V-set_8	e6b3mY2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
S [auth Y]	C1-set_1	e6b3mY1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
R [auth V]	V-set_8	e6b3mV1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
R [auth V]	C1-set_1	e6b3mV2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
L [auth O]	V-set_8	e6b3mO1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
L [auth O]	C1-set_1	e6b3mO2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
K [auth M]	V-set_8	e6b3mM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
K [auth M]	C1-set_1	e6b3mM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
H [auth I]	V-set_8	e6b3mI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
H [auth I]	C1-set_1	e6b3mI2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C	V-set_8	e6b3mC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C	C1-set_1	e6b3mC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth F]	Hemagglutinin_2nd	e6b3mF1	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)
G [auth H]	Hemagglutinin_2nd	e6b3mH1	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)
Q [auth T]	Hemagglutinin_2nd	e6b3mT1	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)
O [auth R]	Hemagglutinin_2nd	e6b3mR1	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 [auth L]	Hemagglutinin_2nd	e6b3mL1	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)
B	Hemagglutinin_2nd	e6b3mB1	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)
A	Hemagglutinin_1st	e6b3mA1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
D [auth E]	Hemagglutinin_1st	e6b3mE1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
F [auth G]	Hemagglutinin_1st	e6b3mG1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
P [auth S]	Hemagglutinin_1st	e6b3mS1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
N [auth Q]	Hemagglutinin_1st	e6b3mQ1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
I [auth K]	Hemagglutinin_1st	e6b3mK1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
X [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
W	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
V [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
U [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
T [auth U]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
M [auth P]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
S [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
R [auth V]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
L [auth O]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
K [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
H [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth F]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
G [auth H]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
Q [auth T]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
O [auth R]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
J [auth L]	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)
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)
D [auth E]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
D [auth E]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
F [auth G]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
F [auth G]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
P [auth S]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
P [auth S]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
N [auth Q]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
N [auth Q]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
I [auth K]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
I [auth K]	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
M [auth P], T [auth U], U [auth J], V [auth D], W, M [auth P], T [auth U], U [auth J], V [auth D], W, X [auth N]	Fab 70-1F02	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202548-0)
C, H [auth I], K [auth M], L [auth O], R [auth V], C, H [auth I], K [auth M], L [auth O], R [auth V], S [auth Y]	Fab 70-1F02	VH-CH1	Homo sapiens (human)	IGHV1-6901, IGHV1-6912, IGHV1-6913, IGHV1-69D01, IGHV1-6915, IGHJ301, IGHJ302, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202548-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
M [auth P], T [auth U], U [auth J], V [auth D], W, M [auth P], T [auth U], U [auth J], V [auth D], W, X [auth N]	Light Chain	IGKV3	Kappa	hemagglutinin ha2 \| hemagglutinin ha1	SAbDab (2025-12-12)
C, H [auth I], K [auth M], L [auth O], R [auth V], C, H [auth I], K [auth M], L [auth O], R [auth V], S [auth Y]	Heavy Chain	IGHV1	-	hemagglutinin ha2 \| hemagglutinin ha1	SAbDab (2025-12-12)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E [auth F], G [auth H], J [auth L], O [auth R], B, E [auth F], G [auth H], J [auth L], O [auth R], Q [auth T]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family
A, D [auth E], F [auth G], I [auth K], N [auth Q], A, D [auth E], F [auth G], I [auth K], N [auth Q], P [auth S]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M [auth P], T [auth U], U [auth J], V [auth D], W, M [auth P], T [auth U], U [auth J], V [auth D], W, X [auth N]	70-1F02 Fab Light Chain	-	-	-
C, H [auth I], K [auth M], L [auth O], R [auth V], C, H [auth I], K [auth M], L [auth O], R [auth V], S [auth Y]	70-1F02 Fab Heavy Chain	-	-	-
B, E [auth F], G [auth H], J [auth L], O [auth R], B, E [auth F], G [auth H], J [auth L], O [auth R], Q [auth T]	Hemagglutinin HA2	host cell surface binding binding host cell surface receptor binding	membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane viral process cellular process cellular component organization or biogenesis membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle endocytosis involved in viral entry into host cell biological process involved in interaction with host membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane viral process cellular process cellular component organization or biogenesis membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle endocytosis involved in viral entry into host cell biological process involved in interaction with host biological process involved in symbiotic interaction	virion component viral membrane viral envelope
A, D [auth E], F [auth G], I [auth K], N [auth Q], A, D [auth E], F [auth G], I [auth K], N [auth Q], P [auth S]	Hemagglutinin HA1	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	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E [auth F], G [auth H], J [auth L], O [auth R], B, E [auth F], G [auth H], J [auth L], O [auth R], Q [auth T]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
B, E [auth F], G [auth H], J [auth L], O [auth R], B, E [auth F], G [auth H], J [auth L], O [auth R], Q [auth T]	IPR000386	Haemagglutinin, influenzavirus B	Family
A, D [auth E], F [auth G], I [auth K], N [auth Q], A, D [auth E], F [auth G], I [auth K], N [auth Q], P [auth S]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A, D [auth E], F [auth G], I [auth K], N [auth Q], A, D [auth E], F [auth G], I [auth K], N [auth Q], P [auth S]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A, D [auth E], F [auth G], I [auth K], N [auth Q], A, D [auth E], F [auth G], I [auth K], N [auth Q], P [auth S]	IPR000149	Haemagglutinin, influenzavirus A	Family
A, D [auth E], F [auth G], I [auth K], N [auth Q], A, D [auth E], F [auth G], I [auth K], N [auth Q], P [auth S]	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily