3IXX | pdb_00003ixx

The pseudo-atomic structure of West Nile immature virus in complex with Fab fragments of the anti-fusion loop antibody E53

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	C1-set_4	e3ixxJ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
J	V-set	e3ixxJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
H	C1-set_4	e3ixxH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
H	V-set	e3ixxH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
I	C1-set_1	e3ixxI2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
I	V-set_12	e3ixxI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
G	C1-set_1	e3ixxG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
G	V-set_12	e3ixxG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
F	Flavi_propep	e3ixxF1	A: beta sandwiches	X: HSP40/DnaJ peptide-binding domain (From Topology)	H: HSP40/DnaJ peptide-binding domain (From Topology)	T: HSP40/DnaJ peptide-binding domain	F: Flavi_propep	ECOD (1.6)
E	Flavi_propep	e3ixxE1	A: beta sandwiches	X: HSP40/DnaJ peptide-binding domain (From Topology)	H: HSP40/DnaJ peptide-binding domain (From Topology)	T: HSP40/DnaJ peptide-binding domain	F: Flavi_propep	ECOD (1.6)
D	Flavi_propep	e3ixxD1	A: beta sandwiches	X: HSP40/DnaJ peptide-binding domain (From Topology)	H: HSP40/DnaJ peptide-binding domain (From Topology)	T: HSP40/DnaJ peptide-binding domain	F: Flavi_propep	ECOD (1.6)
C	Flavi_glycop_C	e3ixxC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
C	Flavi_glycoprot	e3ixxC2	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: Flavi_glycoprot	ECOD (1.6)
B	Flavi_glycop_C	e3ixxB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
B	Flavi_glycoprot	e3ixxB2	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: Flavi_glycoprot	ECOD (1.6)
A	Flavi_glycop_C	e3ixxA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_glycop_C	ECOD (1.6)
A	Flavi_glycoprot	e3ixxA2	A: beta complex topology	X: Viral glycoprotein, central and dimerisation domains-like	H: Viral glycoprotein, central and dimerisation domains (From Topology)	T: Viral glycoprotein, central and dimerisation domains	F: Flavi_glycoprot	ECOD (1.6)

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
H, J	Fab E53	L-KAPPA	Mus musculus (house mouse)	IGKV4-5901, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202549-0)
G, I	Fab E53	VH-CH1	Mus musculus (house mouse)	IGHV7-302, IGHJ101, IGHJ102, IGHG2A01, IGHG2A*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202549-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
H, J	Light Chain	IGKV4	Kappa	envelope protein e, peptide pr \| envelope protein e	SAbDab (2025-12-19)
G, I	Heavy Chain	IGHV7	-	envelope protein e, peptide pr \| envelope protein e	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, E, F	PF01570	Flavivirus polyprotein propeptide (Flavi_propep)	Flavivirus polyprotein propeptide	-	Family
A, B, C	PF00869	Flavivirus glycoprotein, central and dimerisation domains (Flavi_glycoprot)	Flavivirus glycoprotein, central and dimerisation domains		Domain
A, B, C	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
H, J	E53 Fab Fragment (chain L)	-	-	-
G, I	E53 Fab Fragment (chain H)	-	-	-
D, E, F	Peptide pr	RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding double-stranded RNA binding binding nucleic acid binding RNA-directed RNA polymerase activity RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding double-stranded RNA binding binding nucleic acid binding RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity endopeptidase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity protein binding protein dimerization activity cation binding metal ion binding S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity mRNA methyltransferase activity structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT activity symbiont-mediated perturbation of host process symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy 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 immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis protein metabolic process	cellular anatomical structure 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 host cell cytoplasm host cell part host cell endomembrane system host intracellular region cellular anatomical structure 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 host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane viral capsid virion component host cell perinuclear region of cytoplasm virion membrane extracellular region host cell nucleus
A, B, C	Envelope protein E	RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding double-stranded RNA binding binding nucleic acid binding RNA-directed RNA polymerase activity RNA methyltransferase activity O-methyltransferase activity methyltransferase cap1 activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding double-stranded RNA binding binding nucleic acid binding RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity endopeptidase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity protein binding protein dimerization activity cation binding metal ion binding S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity mRNA methyltransferase activity structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT activity symbiont-mediated perturbation of host process symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy 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 immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis protein metabolic process	cellular anatomical structure 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 host cell cytoplasm host cell part host cell endomembrane system host intracellular region cellular anatomical structure 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 host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane viral capsid virion component host cell perinuclear region of cytoplasm virion membrane extracellular region host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E, F	IPR000208	RNA-directed RNA polymerase, fingers/palm subdomains, flavivirus	Domain
D, E, F	IPR014756	Immunoglobulin E-set	Homologous Superfamily
D, E, F	IPR001122	Capsid protein C, flavivirus	Domain
D, E, F	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
D, E, F	IPR014412	Genome polyprotein, Flavivirus	Family
D, E, F	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
D, E, F	IPR011492	Non-structural protein NS3-like, DEAD-box helicase, flavivirus	Domain
D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D, E, F	IPR026490	mRNA cap 0/1 methyltransferase	Domain
D, E, F	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
D, E, F	IPR001650	Helicase, C-terminal domain-like	Domain
D, E, F	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
D, E, F	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
D, E, F	IPR000752	Flavivirus non-structural protein NS2A	Domain
D, E, F	IPR047530	RNA-dependent RNA polymerase, flavivirus	Domain
D, E, F	IPR049486	Flavivridae NS3 helicase, C-terminal helical domain	Domain
D, E, F	IPR046811	RNA-directed RNA polymerase, thumb subdomain, flavivirus	Domain
D, E, F	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
D, E, F	IPR002877	Ribosomal RNA methyltransferase, FtsJ domain	Domain
D, E, F	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
D, E, F	IPR000069	Envelope glycoprotein M, flavivirus	Domain
D, E, F	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
D, E, F	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
D, E, F	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
D, E, F	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
D, E, F	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
D, E, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
D, E, F	IPR037172	Flavivirus capsid protein C superfamily	Homologous Superfamily
D, E, F	IPR000404	Flavivirus non-structural protein NS4A	Domain
D, E, F	IPR000487	Non-structural protein NS2B, flavivirus	Domain
D, E, F	IPR001528	Flavivirus non-structural protein NS4B	Domain
D, E, F	IPR001157	Non-structural protein NS1, flavivirus	Domain
D, E, F	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
D, E, F	IPR001850	Non-structural protein NS3, peptidase S7, flavivirus	Domain
D, E, F	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
D, E, F	IPR002535	Flavivirus polyprotein propeptide	Domain
D, E, F	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, B, C	IPR000208	RNA-directed RNA polymerase, fingers/palm subdomains, flavivirus	Domain
A, B, C	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C	IPR001122	Capsid protein C, flavivirus	Domain
A, B, C	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
A, B, C	IPR014412	Genome polyprotein, Flavivirus	Family
A, B, C	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
A, B, C	IPR011492	Non-structural protein NS3-like, DEAD-box helicase, flavivirus	Domain
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C	IPR026490	mRNA cap 0/1 methyltransferase	Domain
A, B, C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
A, B, C	IPR000752	Flavivirus non-structural protein NS2A	Domain
A, B, C	IPR047530	RNA-dependent RNA polymerase, flavivirus	Domain
A, B, C	IPR049486	Flavivridae NS3 helicase, C-terminal helical domain	Domain
A, B, C	IPR046811	RNA-directed RNA polymerase, thumb subdomain, flavivirus	Domain
A, B, C	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
A, B, C	IPR002877	Ribosomal RNA methyltransferase, FtsJ domain	Domain
A, B, C	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
A, B, C	IPR000069	Envelope glycoprotein M, flavivirus	Domain
A, B, C	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
A, B, C	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
A, B, C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
A, B, C	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
A, B, C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C	IPR037172	Flavivirus capsid protein C superfamily	Homologous Superfamily
A, B, C	IPR000404	Flavivirus non-structural protein NS4A	Domain
A, B, C	IPR000487	Non-structural protein NS2B, flavivirus	Domain
A, B, C	IPR001528	Flavivirus non-structural protein NS4B	Domain
A, B, C	IPR001157	Non-structural protein NS1, flavivirus	Domain
A, B, C	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
A, B, C	IPR001850	Non-structural protein NS3, peptidase S7, flavivirus	Domain
A, B, C	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C	IPR002535	Flavivirus polyprotein propeptide	Domain
A, B, C	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain