4YPG

Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody

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
Thera-SAbDab Antibody Annotation
Protein Family 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)
F [auth L]	d4ypgl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d4ypgl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4ypga1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4ypga2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4ypgb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth H]	d4ypgh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4ypgc1	All alpha proteins	4-helical cytokines	4-helical cytokines	Interferons/interleukin-10 (IL-10)	Interferon-alpha 2a	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4ypgc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4ypgd1	All alpha proteins	4-helical cytokines	4-helical cytokines	Interferons/interleukin-10 (IL-10)	Interferon-alpha 2a	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4ypgd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	8037129	3001717	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	4-helical cytokines	8037129	3001717	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)
F [auth L]	C1-set_4	e4ypgL1	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)
F [auth L]	V-set	e4ypgL2	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)
A	C1-set_4	e4ypgA1	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)
A	V-set	e4ypgA2	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)
B	V-set_8	e4ypgB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B	C1-set_1	e4ypgB2	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)
E [auth H]	V-set_8	e4ypgH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth H]	C1-set_1	e4ypgH2	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)
C	Interferon	e4ypgC1	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)
D	Interferon	e4ypgD1	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)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	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)
E [auth H]	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)
D	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
A, F [auth L]	INN name	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B, E [auth H]	INN name	VH-CH1	Homo sapiens (human)	IGHV1-1801, IGHV1-1804, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
C, D	INN name	IFNA2	Homo sapiens (human)	IFNA2*01	R-LIKE-DOMAIN IFNA2 (Pr24-188)	RPI	IFNA2	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, F [auth L]	Light Chain	IGKV3	Kappa	interferon alpha-2	SAbDab (2024-04-19)
B, E [auth H]	Heavy Chain	IGHV1	-	interferon alpha-2	SAbDab (2024-04-19)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A, F [auth L]	Sifalimumab	IFNA1	Therapeutic SAbDab (2024-04-19)
B, E [auth H]	Sifalimumab	IFNA1	Therapeutic SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F [auth L]	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, F [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
C, D	PF00143	Interferon alpha/beta domain (Interferon)	Interferon alpha/beta domain	Type I interferons (alpha, beta) belong to the larger helical cytokine superfamily,which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, F [auth L]	Sifalimumab light chain	-	-	extracellular region cellular anatomical entity
B, E [auth H]	Sifalimumab heavy chain	-	-	-
C, D	Interferon alpha-2	protein-containing complex binding binding protein 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	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process cellular response to stimulus response to organic substance response to stimulus cell surface receptor signaling pathway signaling response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to organic substance signal transduction developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development leukocyte differentiation immune response adaptive immune response natural killer cell activation cell activation involved in immune response immune effector process natural killer cell activation involved in immune response leukocyte activation involved in immune response lymphocyte activation involved in immune response humoral immune response response to dsRNA response to nitrogen compound response to exogenous dsRNA response to organic cyclic compound regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation regulation of cell differentiation regulation of cell development negative regulation of cell adhesion multicellular organism development negative regulation of T cell differentiation T cell activation T cell differentiation regulation of immune system process negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of lymphocyte differentiation negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of developmental process negative regulation of lymphocyte activation leukocyte cell-cell adhesion regulation of T cell differentiation cell adhesion cell-cell adhesion regulation of multicellular organismal process regulation of cell-cell adhesion negative regulation of cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development negative regulation of developmental process regulation of cell adhesion regulation of T cell activation negative regulation of cell activation negative regulation of cell development negative regulation of immune system process regulation of hemopoiesis regulation of lymphocyte activation negative regulation of interleukin-5 production regulation of interleukin-5 production regulation of cytokine production cytokine production interleukin-5 production negative regulation of cytokine production negative regulation of gene expression apoptotic process cell death programmed cell death cell-cell signaling cell surface receptor signaling pathway via STAT biological process involved in interspecies interaction between organisms negative regulation of viral life cycle viral life cycle modulation by symbiont of entry into host biological process involved in interaction with host biological process involved in symbiotic interaction regulation of viral entry into host cell regulation of viral life cycle regulation of viral process negative regulation of viral process symbiont entry into host cell viral process symbiont entry into host negative regulation of viral entry into host cell regulation of biological process involved in symbiotic interaction cell population proliferation B cell proliferation leukocyte proliferation mononuclear cell proliferation lymphocyte proliferation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity T-helper 2 cell cytokine production negative regulation of lymphocyte mediated immunity T cell cytokine production type 2 immune response regulation of T-helper 2 cell cytokine production regulation of type 2 immune response leukocyte mediated immunity negative regulation of T-helper 2 cell cytokine production regulation of T cell mediated immunity negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response regulation of adaptive immune response negative regulation of immune response negative regulation of immune effector process negative regulation of adaptive immune response negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains negative regulation of type 2 immune response regulation of leukocyte mediated immunity negative regulation of production of molecular mediator of immune response regulation of response to stimulus regulation of immune response regulation of production of molecular mediator of immune response negative regulation of T cell mediated immunity negative regulation of T cell cytokine production regulation of T cell cytokine production CD4-positive, alpha-beta T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains cytokine production involved in immune response production of molecular mediator of immune response negative regulation of response to stimulus regulation of lymphocyte mediated immunity negative regulation of leukocyte mediated immunity defense response response to stress inflammatory response T cell activation involved in immune response response to other organism defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to external biotic stimulus response to virus interleukin-13 production negative regulation of interleukin-13 production regulation of interleukin-13 production cellular response to virus positive regulation of phosphorylation regulation of peptidyl-serine phosphorylation regulation of signal transduction positive regulation of phosphate metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification regulation of receptor signaling pathway via JAK-STAT positive regulation of macromolecule metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation positive regulation of peptidyl-serine phosphorylation of STAT protein protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process serine phosphorylation of STAT protein macromolecule modification regulation of phosphorus metabolic process regulation of receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of peptidyl-serine phosphorylation of STAT protein positive regulation of cellular metabolic process peptidyl-serine modification positive regulation of protein modification process peptidyl-serine phosphorylation protein metabolic process positive regulation of cellular process regulation of signaling organonitrogen compound metabolic process positive regulation of peptidyl-serine phosphorylation regulation of cell communication regulation of phosphorylation cell surface receptor signaling pathway via JAK-STAT interferon-mediated signaling pathway cellular response to type I interferon innate immune response type I interferon-mediated signaling pathway response to type I interferon	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth L]	IPR003597	Immunoglobulin C1-set	Domain
A, F [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, F [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, F [auth L]	IPR003599	Immunoglobulin subtype	Domain
A, F [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
A, F [auth L]	IPR007110	Immunoglobulin-like domain	Domain
A, F [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C, D	IPR000471	Interferon alpha/beta/delta	Family
C, D	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P01563	hepatitis C virus infection chronic myelogenous leukemia, BCR-ABL1 positive plasma cell myeloma renal cell carcinoma essential thrombocythemia neutropenia transitional cell carcinoma Vogt-Koyanagi-Harada disease Stevens-Johnson syndrome thrombocytopenia melanoma leukopenia follicular lymphoma glioblastoma acquired polycythemia vera hepatitis C virus infection chronic myelogenous leukemia, BCR-ABL1 positive plasma cell myeloma renal cell carcinoma essential thrombocythemia neutropenia transitional cell carcinoma Vogt-Koyanagi-Harada disease Stevens-Johnson syndrome thrombocytopenia melanoma leukopenia follicular lymphoma glioblastoma acquired polycythemia vera squamous cell carcinoma adult T-cell leukemia/lymphoma epithelioid hemangioendothelioma hypertriglyceridemia Fatigue sarcomatoid renal cell carcinoma urinary bladder cancer somatization disorder hepatitis anemia stomatitis melancholia thyroid adenoma Raynaud disease endogenous depression Hodgkins lymphoma myocardial infarction retinal detachment intestinal perforation chronic hepatitis B virus infection collecting duct carcinoma giant cell glioblastoma somatoform disorder papillary renal cell carcinoma hepatitis B virus infection substance withdrawal syndrome retinal disease kidney failure chromophobe renal cell carcinoma colorectal cancer skin disease hemolytic anemia polyomavirus infectious disease pterygium anterior ischemic optic neuropathy thyroid gland carcinoma renal carcinoma myeloid neoplasm reticulum cell sarcoma neurotic disorder toxic epidermal necrolysis non-Hodgkin lymphoma colorectal carcinoma acute kidney failure pancreatic neoplasm acute T cell leukemia depressive disorder anxiety disorder Hodgkin's lymphoma, lymphocytic-histiocytic predominance cancer urinary bladder neoplasm cutaneous melanoma plasma cell neoplasm psychiatric disorder thyroid cancer drug-induced liver injury Hodgkin's lymphoma, mixed cellularity epilepsy Huntington disease familial polycythemia nodular lymphocyte predominant Hodgkin lymphoma fatty liver disease sarcoidosis chronic hepatitis C virus infection clear cell renal carcinoma lymphosarcoma malignant pancreatic neoplasm diarrheal disease Hodgkin's lymphoma, lymphocytic depletion

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.