4MHH | pdb_00004mhh

Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/Viet Nam/1203/2004 (H5N1)

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)
I [auth F]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087918	3001616	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087918	3001616	SCOP2B (2022-06-29)
G [auth B]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087918	3001616	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087734	3001342	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087734	3001342	SCOP2B (2022-06-29)
A	SCOP2 Family	Influenza hemagglutinin headpiece	8087733	4002506	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Influenza hemagglutinin domain-like	8087734	3001342	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth J]	His_biosynth	e4mhhJ1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (develop294)
K [auth G]	His_biosynth	e4mhhG1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (develop294)
J [auth H]	ATPaseInh_sub_z	e4mhhH1	A: alpha bundles	X: Flavodoxin-like	H: FXYD family	T: FXYD family	F: ATPaseInh_sub_z	ECOD (develop294)
F [auth K]	His_biosynth	e4mhhK1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (develop294)
E [auth I]	His_biosynth	e4mhhI1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (develop294)
D [auth L]	ATPaseInh_sub_z	e4mhhL1	A: alpha bundles	X: Flavodoxin-like	H: FXYD family	T: FXYD family	F: ATPaseInh_sub_z	ECOD (develop294)
C [auth E]	His_biosynth	e4mhhE1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (develop294)
B [auth C]	His_biosynth	e4mhhC1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: His_biosynth	ECOD (develop294)
A	ATPaseInh_sub_z	e4mhhA1	A: alpha bundles	X: Flavodoxin-like	H: FXYD family	T: FXYD family	F: ATPaseInh_sub_z	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth F]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
H [auth D]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
G [auth B]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
F [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth E]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
C [auth E]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
B [auth C]	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
B [auth C]	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	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)

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
J [auth H], K [auth G], L [auth J]	H5M9 Fab	VH-CH1	Mus musculus (house mouse)	IGHV1-2201, IGHJ101, IGHJ102, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
D [auth L], E [auth I], F [auth K]	H5M9 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV3-501, IGKJ101, IGKJ102, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
J [auth H], K [auth G], L [auth J]	Heavy Chain	IGHV1	-	hemagglutinin ha1 chain	SAbDab (2026-03-20)
D [auth L], E [auth I], F [auth K]	Light Chain	IGKV3	Kappa	hemagglutinin ha1 chain	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth H], K [auth G], L [auth J]	H5M9 antibody, heavy chain (IgG1)	-	-	-
G [auth B], H [auth D], I [auth F]	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 import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular component organization or biogenesis virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host	virion component viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part virion membrane
D [auth L], E [auth I], F [auth K]	H5M9 antibody, light chain (kappa)	-	-	-
A, B [auth C], C [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
G [auth B], H [auth D], I [auth F]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
G [auth B], H [auth D], I [auth F]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
G [auth B], H [auth D], I [auth F]	IPR000149	Haemagglutinin, influenzavirus A	Family
G [auth B], H [auth D], I [auth F]	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
A, B [auth C], C [auth E]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A, B [auth C], C [auth E]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A, B [auth C], C [auth E]	IPR000149	Haemagglutinin, influenzavirus A	Family
A, B [auth C], C [auth E]	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.