4Y5Y | pdb_00004y5y

Diabody 330 complex with EpoR

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4y5ya_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4y5yd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4y5ye_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4y5yb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4y5yc1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4y5yf1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	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	Fibronectin type III	8055513	3002063	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fibronectin type III	8055127	3002063	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Fibronectin type III	8055127	3002063	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Fibronectin type III	8055513	3002063	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	Cupin_1	e4y5yA1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: Cupin_1	ECOD (develop294)
D	Sigma70_r3	e4y5yD1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: Sigma70_r3	ECOD (develop294)
E	Cupin_1	e4y5yE1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: Cupin_1	ECOD (develop294)
B	Sigma70_r3	e4y5yB1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: Sigma70_r3	ECOD (develop294)
C	Cupin_1	e4y5yC1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: Cupin_1	ECOD (develop294)
F	Sigma70_r3	e4y5yF1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: Sigma70_r3	ECOD (develop294)

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)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	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	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D	Heavy Chain	IGHV3	-	erythropoietin receptor	SAbDab (2026-03-20)
B, E	Light Chain	IGLV2	Lambda	erythropoietin receptor	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF09067	Erythropoietin receptor, ligand binding (EpoR_lig-bind)	Erythropoietin receptor, ligand binding	Members of this family interact with erythropoietin (EPO), with subsequent initiation of the downstream chain of events associated with binding of EPO to the receptor, including EPO-induced erythroblast proliferation and differentiation through induc ...	Members of this family interact with erythropoietin (EPO), with subsequent initiation of the downstream chain of events associated with binding of EPO to the receptor, including EPO-induced erythroblast proliferation and differentiation through induction of the JAK2/STAT5 signaling cascade. The domain adopts a secondary structure composed of a short amino-terminal helix, followed by two beta-sandwich regions [1].	Domain
C, F	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	diabody 330 VH domain	-	-	-
B, E	diabody 330 VL domain	-	-	-
C, F	Erythropoietin receptor	molecular transducer activity erythropoietin receptor activity transmembrane signaling receptor activity signaling receptor activity cytokine receptor activity immune receptor activity identical protein binding protein binding binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development heart development circulatory system development multi-multicellular organism process placenta development developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development heart development circulatory system development multi-multicellular organism process placenta development reproductive process maternal process involved in female pregnancy multicellular organismal reproductive process developmental process involved in reproduction tissue development maternal placenta development female pregnancy multi-organism reproductive process decidualization cellular response to stimulus erythropoietin-mediated signaling pathway regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine response to erythropoietin cytokine-mediated signaling pathway cell communication response to peptide cellular response to erythropoietin response to chemical cellular process cellular response to cytokine stimulus signal transduction	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR015152	Growth hormone/erythropoietin receptor, ligand binding	Domain
C, F	IPR009167	Erythropoietin receptor	Family
C, F	IPR003961	Fibronectin type III	Domain
C, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, F	IPR003528	Long hematopoietin receptor, single chain, conserved site	Conserved Site
C, F	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: P19235	polycythemia familial polycythemia melanoma breast carcinoma Neoplasm Metastasis primary familial polycythemia due to EPO receptor mutation thyroid adenoma breast cancer thyroid gland carcinoma large cell medulloblastoma medulloblastoma acquired polycythemia vera ovarian cancer anemia pancreatic intraductal papillary-mucinous neoplasm polycythemia familial polycythemia melanoma breast carcinoma Neoplasm Metastasis primary familial polycythemia due to EPO receptor mutation thyroid adenoma breast cancer thyroid gland carcinoma large cell medulloblastoma medulloblastoma acquired polycythemia vera ovarian cancer anemia pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor cutaneous melanoma erythropoietin polycythemia glioblastoma lung cancer acute erythroid leukemia pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis thyroid cancer dermatomyositis hypertensive disorder malignant glioma osteosarcoma acute erythroleukemia, familial pancreatic intraductal papillary-mucinous carcinoma rheumatoid arthritis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, D	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084
C, F	MLY	Parent Component: LYS RESID: AA0075 , AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084

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.