3IYW | pdb_00003iyw

West Nile virus in complex with Fab fragments of MAb CR4354 (fitted coordinates of envelope proteins and Fab fragments of one icosahedral ASU)

External Resource: Annotation

Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G [auth M]	FAD_binding_4	e3iywM1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
E [auth L]	C1-set	e3iywL1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (develop294)
F [auth K]	FAD_binding_4	e3iywK1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
D [auth H]	C1-set	e3iywH1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (develop294)
C	FAD_binding_4	e3iywC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
B	FAD_binding_4	e3iywB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
A	Arm	e3iywA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arm	ECOD (develop294)

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
E [auth L], G [auth M]	Fab CR4354 mAb, anti-West Nile Virus	L-LAMBDA	Homo sapiens (human)	IGLV1-4401, IGLJ201, IGLJ302, IGLJ301, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
D [auth H], F [auth K]	Fab CR4354 mAb, anti-West Nile Virus	VH-CH1	Homo sapiens (human)	IGHV1-4601, IGHV1-4603, IGHJ501, IGHJ502, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth L], G [auth M]	Light Chain	IGLV1	Lambda	polyprotein	SAbDab (2026-03-20)
D [auth H], F [auth K]	Heavy Chain	IGHV1	-	polyprotein	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth L], G [auth M]	CR4354 Fab fragment X1, light chain L	-	-	-
D [auth H], F [auth K]	CR4354 Fab fragment X1, heavy chain H	-	-	-
A, B, C	Envelope glycoprotein	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 symbiont entry into host cell symbiont entry into host	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, B, C	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
A, B, C	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
A, B, C	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, B, C	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
A, B, C	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
A, B, C	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Transmembrane	Bitopic proteins	Viral membrane fusion glycoprotein	Flavivirus glycoprotein

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth H], F [auth K]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.