4L5F

Crystal Structure of DENV1-E106 Fab bound to DENV-1 Envelope protein DIII

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth H]	d4l5fh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth E]	d4l5fe_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	automated matches	(dengue virus type 1 ) [TaxId: 11053 ],	SCOPe (2.08)
C [auth L]	d4l5fl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth E]	SCOP2 Family	Class II viral fusion proteins C-terminal domain	8073033	4007569	SCOP2 (2022-06-29)
B [auth E]	SCOP2 Superfamily	E set domains	8073034	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)
A [auth H]	PF07654	e4l5fH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A [auth H]	PF07686	e4l5fH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth E]	PF02832	e4l5fE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF02832	ECOD (1.6)
C [auth L]	PF07654	e4l5fL4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth L]	PF07686	e4l5fL3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth E]	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C [auth L]	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 [auth H]	E106 mAb	VH-CH1	Mus musculus (house mouse)	IGHV1-4201, IGHJ201, IGHG2C01, IGHG2C02, IGHG2C*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2C_KAPPA	IMGT (202416-0)
C [auth L]	E106 mAb	L-KAPPA	Mus musculus (house mouse)	IGKV17-12701, IGKJ203, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2C_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV1	-	envelope protein	SAbDab (2024-04-26)
C [auth L]	Light Chain	IGKV17	Kappa	envelope protein	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E]	PF02832	Flavivirus glycoprotein, immunoglobulin-like domain (Flavi_glycop_C)	Flavivirus glycoprotein, immunoglobulin-like domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H]	Heavy chain of E106 antibody (VH and CH1 of IgG2c)	-	-	-
B [auth E]	Envelope protein	protein binding binding protein dimerization activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transport of virus	membrane cellular anatomical entity virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system membrane cellular anatomical entity virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane 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 viral membrane viral envelope
C [auth L]	Light chain of E106 antibody (kappa)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth E]	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
B [auth E]	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
B [auth E]	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
B [auth E]	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
B [auth E]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
B [auth E]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B [auth E]	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
B [auth E]	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
B [auth E]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth E]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.