4UBD | pdb_00004ubd

Crystal structure of a neutralizing human monoclonal antibody with 1968 H3 HA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-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)
L [auth R]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
K [auth N]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
I [auth B]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
C [auth V]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	3001342	SCOP2B (2022-06-29)
F [auth Q]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	3001342	SCOP2B (2022-06-29)
E [auth M]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	3001342	SCOP2B (2022-06-29)
D [auth I]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	3001342	SCOP2B (2022-06-29)
B [auth U]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	3001342	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	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 [auth L]	C1-set_4	e4ubdL2	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 L]	V-set	e4ubdL1	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 P]	C1-set_4	e4ubdP1	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 P]	V-set	e4ubdP2	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	C1-set_4	e4ubdT2	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	V-set	e4ubdT1	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)
R [auth H]	C1-set_4	e4ubdH1	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)
R [auth H]	V-set	e4ubdH2	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)
P [auth X]	C1-set_4	e4ubdX1	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)
P [auth X]	V-set	e4ubdX2	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)
N [auth D]	C1-set_4	e4ubdD2	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)
N [auth D]	V-set	e4ubdD1	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 [auth K]	V-set_8	e4ubdK1	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)
W [auth K]	C1-set_1	e4ubdK2	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)
U [auth O]	V-set_8	e4ubdO1	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)
U [auth O]	C1-set_1	e4ubdO2	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)
S	V-set_8	e4ubdS2	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	C1-set_1	e4ubdS3	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)
Q [auth G]	V-set_8	e4ubdG1	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)
Q [auth G]	C1-set_1	e4ubdG2	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)
O [auth Y]	V-set_8	e4ubdY2	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)
O [auth Y]	C1-set_1	e4ubdY3	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)
M [auth C]	V-set_8	e4ubdC1	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)
M [auth C]	C1-set_1	e4ubdC2	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 R]	Hemagglutinin_2nd	e4ubdR1	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)
K [auth N]	Hemagglutinin_2nd	e4ubdN1	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	e4ubdJ1	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)
I [auth B]	Hemagglutinin_2nd	e4ubdB1	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 [auth F]	Hemagglutinin_2nd	e4ubdF1	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)
C [auth V]	Hemagglutinin_2nd	e4ubdV1	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 E]	Hemagglutinin_1st	e4ubdE1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
F [auth Q]	Hemagglutinin_1st	e4ubdQ1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
E [auth M]	Hemagglutinin_1st	e4ubdM1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
D [auth I]	Hemagglutinin_1st	e4ubdI1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
B [auth U]	Hemagglutinin_1st	e4ubdU1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
A	Hemagglutinin_1st	e4ubdA1	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 L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
V [auth P]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
T	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
R [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
P [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
N [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
W [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
U [auth O]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
S	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
Q [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
O [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
M [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L [auth R]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
K [auth N]	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)
I [auth B]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
H [auth F]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
C [auth V]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
G [auth E]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
F [auth Q]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
E [auth M]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
D [auth I]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
B [auth U]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
A	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
N [auth D], P [auth X], R [auth H], T, V [auth P], N [auth D], P [auth X], R [auth H], T, V [auth P], X [auth L]	Monoclonal antibody	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202542-0)
M [auth C], O [auth Y], Q [auth G], S, U [auth O], M [auth C], O [auth Y], Q [auth G], S, U [auth O], W [auth K]	Monoclonal antibody	VH-CH1	Homo sapiens (human)	IGHV1-1801, IGHV1-1804, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202542-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
N [auth D], P [auth X], R [auth H], T, V [auth P], N [auth D], P [auth X], R [auth H], T, V [auth P], X [auth L]	Light Chain	IGKV3	Kappa	hemagglutinin ha2 chain \| hemagglutinin ha1 chain	SAbDab (2025-10-31)
M [auth C], O [auth Y], Q [auth G], S, U [auth O], M [auth C], O [auth Y], Q [auth G], S, U [auth O], W [auth K]	Heavy Chain	IGHV1	-	hemagglutinin ha2 chain \| hemagglutinin ha1 chain	SAbDab (2025-10-31)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
N [auth D], P [auth X], R [auth H], T, V [auth P], N [auth D], P [auth X], R [auth H], T, V [auth P], X [auth L]	Navivumab	Influenza A HA	Therapeutic SAbDab (2025-10-31)
M [auth C], O [auth Y], Q [auth G], S, U [auth O], M [auth C], O [auth Y], Q [auth G], S, U [auth O], W [auth K]	Navivumab	Influenza A HA	Therapeutic SAbDab (2025-10-31)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth U], D [auth I], E [auth M], F [auth Q], A, B [auth U], D [auth I], E [auth M], F [auth Q], G [auth E]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
N [auth D], P [auth X], R [auth H], T, V [auth P], N [auth D], P [auth X], R [auth H], T, V [auth P], X [auth L]	monoclonal antibody L chain	-	-	-
M [auth C], O [auth Y], Q [auth G], S, U [auth O], M [auth C], O [auth Y], Q [auth G], S, U [auth O], W [auth K]	monoclonal antibody H chain	-	-	-
C [auth V], H [auth F], I [auth B], J, K [auth N], C [auth V], H [auth F], I [auth B], J, K [auth N], L [auth R]	Hemagglutinin HA2 chain	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
A, B [auth U], D [auth I], E [auth M], F [auth Q], A, B [auth U], D [auth I], E [auth M], F [auth Q], G [auth E]	Hemagglutinin HA1 chain	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

InterPro: Protein Family Classification InterPro Database Homepage

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