4YPG | pdb_00004ypg

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)
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)
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)
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)
A	DUF4847	e4ypgA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.1)
F [auth L]	DUF4847	e4ypgL1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.1)
B	DUF4847	e4ypgB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.1)
B	EF-hand_1, EF-hand_6, EF-hand_7	e4ypgB2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)
E [auth H]	DUF4847	e4ypgH1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.1)
E [auth H]	EF-hand_1, EF-hand_6, EF-hand_7	e4ypgH2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)
C	DUF4847	e4ypgC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.1)
D	DUF4847	e4ypgD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: DUF4847	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	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 (202614-0)
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 (202614-0)
C, D	INN name	IFNA2	Homo sapiens (human)	IFNA2*01	R-LIKE-DOMAIN IFNA2 (Pr24-188)	RPI	IFNA2	IMGT (202614-0)

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 (2026-04-17)
B, E [auth H]	Heavy Chain	IGHV1	-	interferon alpha-2	SAbDab (2026-04-17)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A, F [auth L]	Sifalimumab	IFNA1	Therapeutic SAbDab (2026-04-17)
B, E [auth H]	Sifalimumab	IFNA1	Therapeutic SAbDab (2026-04-17)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
B, E [auth H]	Sifalimumab heavy chain	-	-	-
C, D	Interferon alpha-2	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	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process 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 humoral immune response cellular response to stimulus cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway signaling cell communication signal transduction response to chemical response to dsRNA response to nitrogen compound response to exogenous dsRNA regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation regulation of cell development negative regulation of cell adhesion multicellular organism development negative regulation of T cell differentiation T cell activation cell differentiation anatomical structure development T cell differentiation regulation of immune system process negative regulation of hemopoiesis developmental process negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation leukocyte differentiation cellular developmental process regulation of developmental process cell development negative regulation of lymphocyte activation leukocyte cell-cell adhesion regulation of T cell differentiation cell adhesion cell-cell adhesion regulation of multicellular organismal process negative regulation of cell differentiation regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis 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 host-mediated suppression of symbiont invasion host-mediated perturbation of symbiont process modulation of process of another organism cell-cell signaling 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 inflammatory response T cell activation involved in immune response B cell activation B cell activation involved in immune response defense response to virus response to virus interleukin-13 production negative regulation of interleukin-13 production regulation of interleukin-13 production cellular response to virus response to cytokine cytokine-mediated signaling pathway interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus response to peptide type I interferon-mediated signaling pathway response to type I interferon	extracellular matrix cellular anatomical structure external encapsulating structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth L]	IPR003597	Immunoglobulin C1-set	Domain
A, F [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
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]	IPR013106	Immunoglobulin V-set domain	Domain
A, F [auth L]	IPR003599	Immunoglobulin domain subtype	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 thyroid adenoma melancholia Raynaud disease endogenous depression Hodgkins lymphoma retinal detachment intestinal perforation myocardial infarction chronic hepatitis B virus infection giant cell glioblastoma collecting duct carcinoma somatoform disorder papillary renal cell carcinoma hepatitis B virus infection substance withdrawal syndrome retinal disease kidney failure chromophobe renal cell carcinoma skin disease colorectal cancer hemolytic anemia polyomavirus infectious disease pterygium anterior ischemic optic neuropathy thyroid gland carcinoma renal carcinoma reticulum cell sarcoma myeloid neoplasm neurotic disorder non-Hodgkin lymphoma toxic epidermal necrolysis acute kidney failure colorectal carcinoma 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 fatty liver disease sarcoidosis chronic hepatitis C virus infection nodular lymphocyte predominant Hodgkin lymphoma clear cell renal carcinoma lymphosarcoma malignant pancreatic neoplasm diarrheal disease Hodgkin's lymphoma, lymphocytic depletion

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.