Annotations: 1LD4

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ld4a_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
B	d1ld4b_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
C	d1ld4c_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
D	d1ld4d_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
I	d1ld4i_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d1ld4e_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d1ld4f_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G	d1ld4g_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H	d1ld4h_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J	d1ld4j_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
K	d1ld4k_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
L	d1ld4l_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
M	d1ld4m_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
N	d1ld4n_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
O	d1ld4o_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)
P	d1ld4p_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Structural proteins	(Sindbis virus ) [TaxId: 11034 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8071561	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)
A	PF00944	e1ld4A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF00944	ECOD (1.6)
B	PF00944	e1ld4B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF00944	ECOD (1.6)
C	PF00944	e1ld4C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF00944	ECOD (1.6)
D	PF00944	e1ld4D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF00944	ECOD (1.6)
M	PF01589	e1ld4M2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
M	PF01589	e1ld4M1	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: PF01589	ECOD (1.6)
N	PF01589	e1ld4N2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
N	PF01589	e1ld4N1	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: PF01589	ECOD (1.6)
O	PF01589	e1ld4O2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
O	PF01589	e1ld4O1	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: PF01589	ECOD (1.6)
P	PF01589	e1ld4P2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF01589	ECOD (1.6)
P	PF01589	e1ld4P1	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: PF01589	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, F, G, H, I E, F, G, H, I, J, K, L	PF07716	Basic region leucine zipper (bZIP_2)	Basic region leucine zipper	-	Coiled-coil
M, N, O, P	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
A, B, C, D	Coat protein C	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 organic cyclic compound binding nucleic acid binding protein binding ubiquitin-like protein ligase 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 RNA binding binding organic cyclic compound binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transport of virus virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated perturbation of host cellular process response to stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host 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 perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus symbiont-mediated suppression of host signal transduction pathway modulation by symbiont of host process symbiont-mediated suppression of host toll-like receptor signaling pathway organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion membrane membrane cellular anatomical entity viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion membrane T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle viral membrane viral envelope
E, F, G, H, I E, F, G, H, I, J, K, L	GENERAL CONTROL PROTEIN GCN4	TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding transcription regulator activity DNA-binding transcription factor activity mediator complex binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding	response to nutrient levels response to stimulus response to stress response to amino acid starvation response to starvation positive regulation of cellular response to amino acid starvation cellular response to stimulus regulation of response to nutrient levels regulation of cellular process positive regulation of biological process regulation of cellular response to stress cellular response to amino acid starvation positive regulation of response to stimulus cellular response to stress response to nutrient levels response to stimulus response to stress response to amino acid starvation response to starvation positive regulation of cellular response to amino acid starvation cellular response to stimulus regulation of response to nutrient levels regulation of cellular process positive regulation of biological process regulation of cellular response to stress cellular response to amino acid starvation positive regulation of response to stimulus cellular response to stress regulation of response to stress positive regulation of cellular process regulation of biological process biological regulation cellular response to starvation cellular response to nutrient levels regulation of response to stimulus cellular process regulation of cellular response to amino acid starvation positive regulation of response to nutrient levels transcription preinitiation complex assembly positive regulation of macromolecule biosynthetic process regulation of primary metabolic process cellular component biogenesis nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process cellular component assembly transcription by RNA polymerase II organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process RNA polymerase II preinitiation complex assembly metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of RNA polymerase II transcription preinitiation complex assembly regulation of cellular component organization positive regulation of cellular component organization cellular biosynthetic process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular metabolic process cellular component organization protein-DNA complex organization RNA biosynthetic process nucleic acid biosynthetic process regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly organic substance metabolic process positive regulation of biosynthetic process protein-containing complex assembly cellular component organization or biogenesis regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of RNA polymerase II transcription preinitiation complex assembly protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of transcription initiation by RNA polymerase II protein-DNA complex assembly regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II positive regulation of cellular biosynthetic process protein localization localization cellular localization protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to nuclear periphery protein localization to nucleus amino acid biosynthetic process amino acid metabolic process cellular response to nitrogen compound response to organic substance nitrogen catabolite regulation of transcription regulation of nitrogen utilization intracellular nitrogen homeostasis nitrogen catabolite activation of transcription from RNA polymerase II promoter response to organonitrogen compound response to nitrogen compound cellular response to organonitrogen compound chemical homeostasis response to chemical homeostatic process cellular response to endogenous stimulus nitrogen catabolite activation of transcription intracellular chemical homeostasis cellular response to organic substance nitrogen catabolite regulation of transcription from RNA polymerase II promoter response to endogenous stimulus response to nutrient nitrogen utilization cellular response to chemical stimulus cellular homeostasis cellular response to nutrient signaling signal transduction intracellular signal transduction cell communication negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process regulation of ribosomal protein gene transcription by RNA polymerase II negative regulation of ribosomal protein gene transcription by RNA polymerase II	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle
M, N, O, P	Spike glycoprotein E1	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 organic cyclic compound binding nucleic acid binding protein binding ubiquitin-like protein ligase 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 RNA binding binding organic cyclic compound binding nucleic acid binding protein binding ubiquitin-like protein ligase binding enzyme binding structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transport of virus virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated perturbation of host cellular process response to stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host 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 perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus symbiont-mediated suppression of host signal transduction pathway modulation by symbiont of host process symbiont-mediated suppression of host toll-like receptor signaling pathway organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion membrane membrane cellular anatomical entity viral capsid icosahedral viral capsid virion component icosahedral viral capsid, spike host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell cytoplasm host intracellular region virion membrane T=4 icosahedral viral capsid host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle viral membrane viral envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
E, F, G, H, I E, F, G, H, I, J, K, L	IPR004827	Basic-leucine zipper domain	Domain
E, F, G, H, I E, F, G, H, I, J, K, L	IPR046347	Basic-leucine zipper domain superfamily	Homologous Superfamily
M, N, O, P	IPR002533	Alphavirus E3 spike glycoprotein	Domain
M, N, O, P	IPR038055	Flaviviral glycoprotein E, dimerisation domain	Homologous Superfamily
M, N, O, P	IPR014756	Immunoglobulin E-set	Homologous Superfamily
M, N, O, P	IPR042304	Alphavirus E2 glycoprotein, domain A	Homologous Superfamily
M, N, O, P	IPR036253	Flavivirus glycoprotein, central and dimerisation domain superfamily	Homologous Superfamily
M, N, O, P	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
M, N, O, P	IPR042305	Alphavirus E2 glycoprotein, domain B	Homologous Superfamily
M, N, O, P	IPR042306	Alphavirus E2 glycoprotein, domain C	Homologous Superfamily
M, N, O, P	IPR000936	Alphavirus E2 glycoprotein	Family
M, N, O, P	IPR000930	Peptidase S3, togavirin	Domain
M, N, O, P	IPR002548	Alphavirus E1 glycoprotein	Domain
M, N, O, P	IPR000336	Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily	Homologous Superfamily
M, N, O, P	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily