8DWX | pdb_00008dwx

Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J [auth R]	SCOP2B Superfamily	Trypsin-like serine proteases	8071557	3000114	SCOP2B (2022-06-29)
K [auth S]	SCOP2B Superfamily	Trypsin-like serine proteases	8071557	3000114	SCOP2B (2022-06-29)
L [auth T]	SCOP2B Superfamily	Trypsin-like serine proteases	8071557	3000114	SCOP2B (2022-06-29)
I [auth Q]	SCOP2B Superfamily	Trypsin-like serine proteases	8071557	3000114	SCOP2B (2022-06-29)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
Q [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
S [auth Z]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
O [auth V]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
M [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
P [auth U]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
R [auth W]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
T [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth M]	2.60.40.3200	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, A domain	CATH (utative)
H [auth P]	2.60.40.3200	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, A domain	CATH (utative)
G [auth O]	2.60.40.3200	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, A domain	CATH (utative)
F [auth N]	2.60.40.3200	Mainly Beta	Sandwich	Immunoglobulin-like	Alphavirus E2 glycoprotein, A domain	CATH (utative)
A	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)
B	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)
D	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)
C	2.60.40.350	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
N [auth H], O [auth V], Q [auth X], S [auth Z]	Heavy Chain	IGHV4	-	e2 glycoprotein	SAbDab (2025-10-10)
M [auth L], P [auth U], R [auth W], T [auth Y]	Light Chain	IGKV1	Kappa	e2 glycoprotein	SAbDab (2025-10-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth Q], J [auth R], K [auth S], L [auth T]	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
E [auth M], F [auth N], G [auth O], H [auth P]	PF00943	Alphavirus E2 glycoprotein (Alpha_E2_glycop)	Alphavirus E2 glycoprotein	-	Family
A, B, C, D	PF01589	Alphavirus E1 glycoprotein (Alpha_E1_glycop)	Alphavirus E1 glycoprotein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
N [auth H], O [auth V], Q [auth X], S [auth Z]	506.C01 heavy chain	-	-	-
M [auth L], P [auth U], R [auth W], T [auth Y]	506.C01 light chain	-	-	-
I [auth Q], J [auth R], K [auth S], L [auth T]	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 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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle
E [auth M], F [auth N], G [auth O], H [auth P]	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 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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle
A, B, C, D	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 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 virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region virion component virion membrane viral capsid icosahedral viral capsid T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E [auth M] A, B, C, D, E [auth M], F [auth N], G [auth O], H [auth P], I [auth Q], J [auth R], K [auth S], L [auth T]	OPM	Transmembrane	Bitopic proteins	Viral membrane fusion glycoprotein	Alphavirus E1 glycoprotein

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E [auth M] A, B, C, D, E [auth M], F [auth N], G [auth O], H [auth P], I [auth Q], J [auth R], K [auth S], L [auth T]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E [auth M] A, B, C, D, E [auth M], F [auth N], G [auth O], H [auth P], I [auth Q], J [auth R], K [auth S], L [auth T]	MemProtMD	Annotated as membrane protein by MemProtMD