7CVY | pdb_00007cvy

Cryo-EM structure of Chikungunya virus in complex with Fab fragments of mAb CHK-124

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family 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)
L [auth M]	SCOP2B Superfamily	Trypsin-like serine proteases	8101317	3000114	SCOP2B (2022-06-29)
I [auth R]	SCOP2B Superfamily	Trypsin-like serine proteases	8101317	3000114	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Trypsin-like serine proteases	8101317	3000114	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	Trypsin-like serine proteases	8101317	3000114	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth G]	dCMP_cyt_deam_1	e7cvyG01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: dCMP_cyt_deam_1	ECOD (v294.1)
M [auth K]	PA14	e7cvyK1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
J [auth P]	PA14	e7cvyP1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
G [auth A]	PA14	e7cvyA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
D [auth F]	PA14	e7cvyF1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
L [auth M]	PA14	e7cvyM1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
I [auth R]	PA14	e7cvyR1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
F [auth C]	PA14	e7cvyC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
C [auth H]	PA14	e7cvyH1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
T [auth O]	PA14	e7cvyO1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
R [auth J]	PA14	e7cvyJ1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
P [auth T]	PA14	e7cvyT1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
B [auth E]	PA14	e7cvyE1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
S [auth N]	PA14	e7cvyN1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
Q [auth I]	PA14	e7cvyI1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
O [auth S]	PA14	e7cvyS1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)
A [auth D]	PA14	e7cvyD1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: PA14	ECOD (v294.1)

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
B [auth E], P [auth T], R [auth J], T [auth O]	mAb CHK-124	L-KAPPA	Mus musculus (house mouse)	IGKV6-1501, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)
A [auth D], O [auth S], Q [auth I], S [auth N]	mAb CHK-124	VH-CH1	Mus musculus (house mouse)	IGHV6-301, IGHJ401, IGHG2C01, IGHG2C02, IGHG2C*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth E], P [auth T], R [auth J], T [auth O]	Light Chain	IGKV6	Kappa	e2 glycoprotein	SAbDab (2026-04-10)
A [auth D], O [auth S], Q [auth I], S [auth N]	Heavy Chain	IGHV6	-	e2 glycoprotein	SAbDab (2026-04-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth G], H [auth B], K [auth Q], N [auth L]	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
D [auth F], G [auth A], J [auth P], M [auth K]	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family
C [auth H], F [auth C], I [auth R], L [auth M]	PF00944	Alphavirus core protein (Peptidase_S3)	Alphavirus core protein	Also known as coat protein C and capsid protein C. This makes the literature very confusing. Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth G], H [auth B], K [auth Q], N [auth L]	E2 glycoprotein	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 RNA binding binding nucleic acid binding passive transmembrane transporter activity channel activity transporter activity 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 RNA binding binding nucleic acid binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism viral gene expression viral translational frameshifting viral translation transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport cellular process establishment of localization proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell adhesion of symbiont to host	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus
D [auth F], G [auth A], J [auth P], M [auth K]	E1 glycoprotein	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 RNA binding binding nucleic acid binding passive transmembrane transporter activity channel activity transporter activity 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 RNA binding binding nucleic acid binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism viral gene expression viral translational frameshifting viral translation transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport cellular process establishment of localization proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell adhesion of symbiont to host	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus
C [auth H], F [auth C], I [auth R], L [auth M]	Capsid protein	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 RNA binding binding nucleic acid binding passive transmembrane transporter activity channel activity transporter activity 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 RNA binding binding nucleic acid binding passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated suppression of host toll-like receptor signaling pathway symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism viral gene expression viral translational frameshifting viral translation transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport cellular process establishment of localization proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell adhesion of symbiont to host	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell plasma membrane host cell membrane virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host cell Golgi apparatus host cell nucleus
B [auth E], P [auth T], R [auth J], T [auth O]	Fab light chain	-	-	-
A [auth D], O [auth S], Q [auth I], S [auth N]	Fab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR000936	Alphavirus E2 glycoprotein	Family
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR000930	Peptidase S3, togavirin	Domain
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR002548	Alphavirus E1 glycoprotein	Domain
E [auth G], H [auth B], K [auth Q], N [auth L]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth F], G [auth A], J [auth P], M [auth K]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
D [auth F], G [auth A], J [auth P], M [auth K]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
D [auth F], G [auth A], J [auth P], M [auth K]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
D [auth F], G [auth A], J [auth P], M [auth K]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
D [auth F], G [auth A], J [auth P], M [auth K]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
D [auth F], G [auth A], J [auth P], M [auth K]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
D [auth F], G [auth A], J [auth P], M [auth K]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
D [auth F], G [auth A], J [auth P], M [auth K]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
D [auth F], G [auth A], J [auth P], M [auth K]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
D [auth F], G [auth A], J [auth P], M [auth K]	IPR000936	Alphavirus E2 glycoprotein	Family
D [auth F], G [auth A], J [auth P], M [auth K]	IPR000930	Peptidase S3, togavirin	Domain
D [auth F], G [auth A], J [auth P], M [auth K]	IPR002548	Alphavirus E1 glycoprotein	Domain
D [auth F], G [auth A], J [auth P], M [auth K]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H], F [auth C], I [auth R], L [auth M]	IPR002533	Alphavirus E3 spike glycoprotein	Domain
C [auth H], F [auth C], I [auth R], L [auth M]	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
C [auth H], F [auth C], I [auth R], L [auth M]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
C [auth H], F [auth C], I [auth R], L [auth M]	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
C [auth H], F [auth C], I [auth R], L [auth M]	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
C [auth H], F [auth C], I [auth R], L [auth M]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
C [auth H], F [auth C], I [auth R], L [auth M]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C [auth H], F [auth C], I [auth R], L [auth M]	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
C [auth H], F [auth C], I [auth R], L [auth M]	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
C [auth H], F [auth C], I [auth R], L [auth M]	IPR000936	Alphavirus E2 glycoprotein	Family
C [auth H], F [auth C], I [auth R], L [auth M]	IPR000930	Peptidase S3, togavirin	Domain
C [auth H], F [auth C], I [auth R], L [auth M]	IPR002548	Alphavirus E1 glycoprotein	Domain
C [auth H], F [auth C], I [auth R], L [auth M]	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily