5VIG

Crystal structure of anti-Zika antibody Z006 bound to Zika virus 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]	d5vigh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d5viga_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d5vigl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d5vigl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d5vigb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d5vigb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth Z]	d5vigz_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	automated matches	ZIKV (Zika virus ) [TaxId: 64320 ],	SCOPe (2.08)
F [auth G]	d5vigg_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Class II viral fusion proteins C-terminal domain	automated matches	ZIKV (Zika virus ) [TaxId: 64320 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth Z]	SCOP2B Superfamily	E set domains	8073024	3000070	SCOP2B (2022-06-29)
F [auth G]	SCOP2 Family	Class II viral fusion proteins C-terminal domain	8073023	4007569	SCOP2 (2022-06-29)
F [auth G]	SCOP2 Superfamily	E set domains	8073024	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]	C1-set_1	e5vigH1	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)
A [auth H]	V-set_12	e5vigH2	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)
D [auth A]	C1-set_1	e5vigA2	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)
D [auth A]	V-set_12	e5vigA1	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)
B [auth L]	C1-set_4	e5vigL1	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)
B [auth L]	V-set	e5vigL2	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)
E [auth B]	C1-set_4	e5vigB2	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)
E [auth B]	V-set	e5vigB1	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)
C [auth Z]	Flavi_glycop_C	e5vigZ1	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)
F [auth G]	Flavi_glycop_C	e5vigG1	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)

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)
D [auth A]	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 B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth Z]	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
F [auth G]	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
A [auth H], D [auth A]	Fab Z006	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHV3-2303, IGHV3-23D01, IGHJ101, IGHJ501, IGHJ502, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202450-0)
B [auth L], E [auth B]	Fab Z006	L-KAPPA	Homo sapiens (human)	IGKV1-501, IGKV1-503, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202450-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], D [auth A]	Heavy Chain	IGHV3	-	zika virus envelope protein diii	SAbDab (2024-12-20)
B [auth L], E [auth B]	Light Chain	IGKV1	Kappa	zika virus envelope protein diii	SAbDab (2024-12-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth H], D [auth A]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A [auth H], D [auth A]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B [auth L], E [auth B]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B [auth L], E [auth B]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], D [auth A]	Fab heavy chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex
B [auth L], E [auth B]	Fab light chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
C [auth Z], F [auth G]	Zika virus envelope protein DIII	RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity adenyl ribonucleotide binding RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic 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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity protein binding protein dimerization activity cation binding metal ion binding RNA methyltransferase activity O-methyltransferase activity transferase activity, transferring one-carbon groups mRNA (nucleoside-2'-O-)-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity mRNA methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-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 defense response symbiont-mediated perturbation of host process modulation by virus of host process virus-mediated perturbation of host defense response modulation of process of another organism modulation by virus of host cellular process response to host defenses response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated perturbation of host signal transduction 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 symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT 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 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 cellular anatomical structure 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 capsid virion component virion membrane extracellular region host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth H], D [auth A]	IPR003597	Immunoglobulin C1-set	Domain
A [auth H], D [auth A]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth H], D [auth A]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth H], D [auth A]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth H], D [auth A]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth H], D [auth A]	IPR007110	Immunoglobulin-like domain	Domain
A [auth H], D [auth A]	IPR050380	Immune Recognition and Response Modulators	Family
A [auth H], D [auth A]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B [auth L], E [auth B]	IPR003597	Immunoglobulin C1-set	Domain
B [auth L], E [auth B]	IPR050150	Immunoglobulin Variable Light Chain	Family
B [auth L], E [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth L], E [auth B]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L], E [auth B]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth L], E [auth B]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth L], E [auth B]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L], E [auth B]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth Z], F [auth G]	IPR000208	RNA-directed RNA polymerase, fingers/palm subdomains, flavivirus	Domain
C [auth Z], F [auth G]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
C [auth Z], F [auth G]	IPR001122	Capsid protein C, flavivirus	Domain
C [auth Z], F [auth G]	IPR027287	Glycoprotein E, immunoglobulin-like domain, flavivirus	Domain
C [auth Z], F [auth G]	IPR014412	Genome polyprotein, Flavivirus	Family
C [auth Z], F [auth G]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
C [auth Z], F [auth G]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth Z], F [auth G]	IPR026490	mRNA cap 0/1 methyltransferase	Domain
C [auth Z], F [auth G]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C [auth Z], F [auth G]	IPR001650	Helicase, C-terminal domain-like	Domain
C [auth Z], F [auth G]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
C [auth Z], F [auth G]	IPR013755	Flaviviral glycoprotein E, central domain, subdomain 1	Homologous Superfamily
C [auth Z], F [auth G]	IPR000752	Flavivirus non-structural protein NS2A	Domain
C [auth Z], F [auth G]	IPR047530	RNA-dependent RNA polymerase, flavivirus	Domain
C [auth Z], F [auth G]	IPR049486	Flavivridae NS3 helicase, C-terminal helical domain	Domain
C [auth Z], F [auth G]	IPR046811	RNA-directed RNA polymerase, thumb subdomain, flavivirus	Domain
C [auth Z], F [auth G]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
C [auth Z], F [auth G]	IPR002877	Ribosomal RNA methyltransferase, FtsJ domain	Domain
C [auth Z], F [auth G]	IPR038302	Envelope glycoprotein M superfamily, flavivirus	Homologous Superfamily
C [auth Z], F [auth G]	IPR000069	Envelope glycoprotein M, flavivirus	Domain
C [auth Z], F [auth G]	IPR011492	Non-structural protein NS3-like, DEAD box helicase, flavivirus	Domain
C [auth Z], F [auth G]	IPR038345	Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily	Homologous Superfamily
C [auth Z], F [auth G]	IPR038688	Flavivirus polyprotein propeptide superfamily	Homologous Superfamily
C [auth Z], F [auth G]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
C [auth Z], F [auth G]	IPR026470	Flavivirus envelope glycoprotein E, Stem/Anchor domain	Domain
C [auth Z], F [auth G]	IPR011998	Envelope glycoprotein E, central and dimerisation domain, flavivirus	Domain
C [auth Z], F [auth G]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth Z], F [auth G]	IPR037172	Flavivirus capsid protein C superfamily	Homologous Superfamily
C [auth Z], F [auth G]	IPR000404	Flavivirus non-structural protein NS4A	Domain
C [auth Z], F [auth G]	IPR000487	Non-structural protein NS2B, flavivirus	Domain
C [auth Z], F [auth G]	IPR001528	Flavivirus non-structural protein NS4B	Domain
C [auth Z], F [auth G]	IPR001157	Non-structural protein NS1, flavivirus	Domain
C [auth Z], F [auth G]	IPR013756	Flaviviral glycoprotein E, central domain, subdomain 2	Homologous Superfamily
C [auth Z], F [auth G]	IPR001850	Non-structural protein NS3, peptidase S7, flavivirus	Domain
C [auth Z], F [auth G]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth Z], F [auth G]	IPR002535	Flavivirus polyprotein propeptide	Domain
C [auth Z], F [auth G]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain