4FFZ | pdb_00004ffz

Crystal Structure of DENV1-E111 fab fragment bound to DENV-1 DIII (Western Pacific-74 strain).

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab 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)
A	SCOP2B Superfamily	E set domains	8100076	3000070	SCOP2B (2022-06-29)
D [auth X]	SCOP2 Family	Class II viral fusion proteins C-terminal domain	8100075	4007569	SCOP2 (2022-06-29)
D [auth X]	SCOP2 Superfamily	E set domains	8100076	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)
C [auth H]	TIM	e4ffzH1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: TIM	ECOD (v294.1)
F [auth Z]	Rrf2	e4ffzZ1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Rrf2	ECOD (v294.1)
B [auth L]	TIM	e4ffzL1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: TIM	ECOD (v294.1)
E [auth Y]	V-set	e4ffzY1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (v294.1)
A	TIM	e4ffzA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: TIM	ECOD (v294.1)
D [auth X]	ABC_tran	e4ffzX1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth Z]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
D [auth X]	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		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
C [auth H], F [auth Z]	DENV1-E111 FAB FRAGMENT	VH-CH1	Mus musculus (house mouse)	IGHV1-7201, IGHJ103, IGHG2C01, IGHG2C02, IGHG2C*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2C_KAPPA	IMGT (202612-0)
B [auth L], E [auth Y]	DENV1-E111 FAB FRAGMENT	L-KAPPA	Mus musculus (house mouse)	IGKV3-1001, IGKJ102, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2C_KAPPA	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H], F [auth Z]	Heavy Chain	IGHV1	-	envelope protein e	SAbDab (2026-03-27)
B [auth L], E [auth Y]	Light Chain	IGKV3	Kappa	envelope protein e	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth H], F [auth Z]	DENV1-E111 fab fragment (heavy chain)	-	-	-
B [auth L], E [auth Y]	DENV1-E111 fab fragment (light chain)	-	-	-
A, D [auth X]	Envelope protein E	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 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	virion component virion membrane 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 cellular anatomical structure host cell cytoplasm host cell part host cell endomembrane system virion component virion membrane 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 cellular anatomical structure host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

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