3UX9 | pdb_00003ux9

Structural insights into a human anti-IFN antibody exerting therapeutic potential for systemic lupus erythematosus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3ux9d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ux9b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3ux9c_	All alpha proteins	4-helical cytokines	4-helical cytokines	Interferons/interleukin-10 (IL-10)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ux9a_	All alpha proteins	4-helical cytokines	4-helical cytokines	Interferons/interleukin-10 (IL-10)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	4-helical cytokines	8070377	3001717	SCOP2B (2022-06-29)
A	SCOP2 Family	Interferons/interleukin-10 (IL-10)	8070376	4000854	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	4-helical cytokines	8070377	3001717	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)
D	V-set_3	e3ux9D6	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D	V-set_12	e3ux9D5	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	V-set_3	e3ux9B4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
B	V-set_12	e3ux9B3	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)
C	Interferon	e3ux9C2	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: Interferon	ECOD (1.6)
A	Interferon	e3ux9A1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: Interferon	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
A	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	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
B, D	scFv, anti-IFN	V-LAMBDA-VH	Homo sapiens (human)	IGLV1-4401, IGLJ302, IGHV3-2304, IGHJ401, IGHJ402, IGHJ403	V-DOMAIN V-LAMBDA, V-DOMAIN VH	IG	SCFV-LAMBDA-HEAVY	IMGT (202546-0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	ScFv antibody	-	-	-
A, C	Interferon alpha-1/13	protein-containing complex binding protein binding binding type I interferon receptor binding signaling receptor binding cytokine receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	response to stimulus immune response immune system process adaptive immune response multicellular organismal process biological process involved in interspecies interaction between organisms lymphocyte activation cell activation involved in immune response response to biotic stimulus leukocyte activation response to stress natural killer cell activation involved in immune response leukocyte activation involved in immune response innate immune response response to stimulus immune response immune system process adaptive immune response multicellular organismal process biological process involved in interspecies interaction between organisms lymphocyte activation cell activation involved in immune response response to biotic stimulus leukocyte activation response to stress natural killer cell activation involved in immune response leukocyte activation involved in immune response innate immune response response to external biotic stimulus lymphocyte activation involved in immune response response to other organism defense response cell activation defense response to symbiont response to external stimulus natural killer cell activation immune effector process defense response to other organism cellular process humoral immune response response to chemical response to dsRNA response to nitrogen compound response to exogenous dsRNA T cell activation involved in immune response T cell activation B cell activation B cell activation involved in immune response defense response to virus response to virus cellular response to virus cellular response to stimulus regulation of cellular process signaling response to cytokine cytokine-mediated signaling pathway cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus signal transduction regulation of biological process cell surface receptor signaling pathway biological regulation response to peptide type I interferon-mediated signaling pathway response to type I interferon	cellular anatomical structure extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR000471	Interferon alpha/beta/delta	Family
A, C	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P01562	VIPoma hepatitis B virus infection adult T-cell leukemia/lymphoma melanoma Liver Cirrhosis, Experimental colorectal cancer skin disease liver cancer pancreatic cholera tubular adenocarcinoma granular cell carcinoma adenocarcinoma cirrhosis of liver epilepsy HIV infectious disease VIPoma hepatitis B virus infection adult T-cell leukemia/lymphoma melanoma Liver Cirrhosis, Experimental colorectal cancer skin disease liver cancer pancreatic cholera tubular adenocarcinoma granular cell carcinoma adenocarcinoma cirrhosis of liver epilepsy HIV infectious disease leukopenia lymphatic system disease AIDS malignant pancreatic neoplasm bipolar disorder microphthalmia with limb anomalies peripheral nervous system disease COVID-19 cutaneous melanoma vaginal cancer hepatitis C virus infection influenza acute T cell leukemia liver disease major depressive disorder arthritic joint disease cancer colorectal carcinoma peripheral neuropathy cribriform carcinoma hepatocellular carcinoma kidney disease liver neoplasm autoimmune disease pancreatic neoplasm pneumonia cribriform carcinoma of breast

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.