5AAM | pdb_00005aam

Structure of a redesigned cross-reactive antibody to dengue virus with increased in vivo potency

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT 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)
D [auth J]	SCOP2B Superfamily	E set domains	8073054	3000070	SCOP2B (2022-06-29)
C	SCOP2 Family	Class II viral fusion proteins C-terminal domain	8073053	4007569	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	E set domains	8073054	3000070	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)
D [auth J]	DHFR_1	e5aamJ1	A: alpha bundles	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: DHFR_1	ECOD (develop294)
C	DHFR_1	e5aamC1	A: alpha bundles	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: DHFR_1	ECOD (develop294)
B	PhyH	e5aamB1	A: alpha bundles	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: PhyH	ECOD (develop294)
A	Peptidase_M24	e5aamA1	A: alpha bundles	X: Repetitive alpha hairpins	H: C2 domain	T: C2 domain	F: Peptidase_M24	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth J]	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	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
A, B	SCFV513, anti-dengue virus	SCFV-HEAVY-KAPPA	Chimeric (chimeric)	IGHV1-1801, IGHV1-1804, IGHJ401, IGHJ402, IGHJ403, IGKV3-501, IGKJ1*01	V-DOMAIN VH, V-DOMAIN V-KAPPA	IG	SCFV-HEAVY-KAPPA	IMGT (202610-0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D [auth J]	ENVELOPE PROTEIN	binding lipid binding structural molecule activity protein binding protein dimerization activity	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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism	viral capsid virion component virion membrane cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm viral capsid virion component virion membrane cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane host cell nucleus viral membrane viral envelope
A, B	SCFV513	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D [auth J]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
C, D [auth J]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
C, D [auth J]	IPR001122	Capsid protein C, flavivirus	Domain
C, D [auth J]	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
C, D [auth J]	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
C, D [auth J]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
C, D [auth J]	IPR000069	Envelope glycoprotein M, flavivirus	Domain
C, D [auth J]	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
C, D [auth J]	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
C, D [auth J]	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
C, D [auth J]	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
C, D [auth J]	IPR037172	Flavivirus capsid protein C superfamily	Homologous Superfamily
C, D [auth J]	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
C, D [auth J]	IPR001157	Non-structural protein NS1, flavivirus	Domain
C, D [auth J]	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
C, D [auth J]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
C, D [auth J]	IPR002535	Flavivirus polyprotein propeptide	Domain

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.