2JIX

Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor

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
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)
B	d2jixb1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	Erythropoietin (EPO) receptor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2jixc1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	Erythropoietin (EPO) receptor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2jixe1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	Erythropoietin (EPO) receptor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2jixd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2jixd2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2jixd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2jixf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2jixf2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2jixf3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2jixh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2jixh2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2jixh3	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)
B	SCOP2B Superfamily	Fibronectin type III	8055127	3002063	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Fibronectin type III	8055513	3002063	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fibronectin type III	8055127	3002063	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fibronectin type III	8055513	3002063	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Fibronectin type III	8055127	3002063	SCOP2B (2022-06-29)
E	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	C1-set_4	e2jixA2	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	e2jixA1	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)
G	C1-set_4	e2jixG2	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)
G	V-set	e2jixG1	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)
I [auth L]	C1-set_4	e2jixL2	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)
I [auth L]	V-set	e2jixL1	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	EpoR_lig-bind	e2jixB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: EpoR_lig-bind	ECOD (1.6)
B	fn3_6	e2jixB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3_6	ECOD (1.6)
C	EpoR_lig-bind	e2jixC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: EpoR_lig-bind	ECOD (1.6)
C	fn3_6	e2jixC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3_6	ECOD (1.6)
E	EpoR_lig-bind	e2jixE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: EpoR_lig-bind	ECOD (1.6)
E	fn3_6	e2jixE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3_6	ECOD (1.6)
D	V-set_8	e2jixD1	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)
D	C1-set_1	e2jixD2	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)
F	V-set_8	e2jixF1	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)
F	C1-set_1	e2jixF2	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)
H	V-set_8	e2jixH1	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)
H	C1-set_1	e2jixH2	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)

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)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [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)
C	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)
D	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)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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, G, I [auth L]	ABT-007 Fab	L-KAPPA	Homo sapiens (human)	IGKV1-1701, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202449-0)
B, C, E	EPOR (Erythropoietin receptor)	2F-DOMAIN	Homo sapiens (human)	EPOR*01	F-LIKE-DOMAIN F-DOMAIN	RPI	2F-DOMAIN	IMGT (202449-0)
D, F, H	ABT-007 Fab	VH-CH1	Homo sapiens (human)	IGHV4-5901, IGHV4-5903, IGHV4-5908, IGHV4-408, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202449-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, G, I [auth L]	Light Chain	IGKV1	Kappa	erythropoietin receptor \| erythropoietin receptor, erythropoietin receptor	SAbDab (2024-12-13)
D, F, H	Heavy Chain	IGHV4	-	erythropoietin receptor, erythropoietin receptor \| erythropoietin receptor	SAbDab (2024-12-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, G, I [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, G, I [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B, C, E	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
B, C, E	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain	-	Domain
D, F, H	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
D, F, H	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, G, I [auth L]	ABT-007 FAB FRAGMENT	-	-	cellular anatomical structure extracellular region
B, C, E	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	regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process cellular process positive regulation of cellular process developmental process multicellular organism development multicellular organismal process head development central nervous system development regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process cellular process positive regulation of cellular process 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 cellular response to stimulus response to stimulus cell surface receptor signaling pathway signaling response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular response to cytokine stimulus signal transduction 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 erythropoietin-mediated signaling pathway response to erythropoietin cellular response to erythropoietin cellular developmental process hemopoiesis cell differentiation cell development	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 membrane-bounded organelle intracellular organelle lumen nuclear speck 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 membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen extracellular region
D, F, H	ABT-007 FAB FRAGMENT	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, G, I [auth L]	IPR003597	Immunoglobulin C1-set	Domain
A, G, I [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
A, G, I [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, G, I [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, G, I [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
A, G, I [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
A, G, I [auth L]	IPR007110	Immunoglobulin-like domain	Domain
A, G, I [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B, C, E	IPR015152	Growth hormone/erythropoietin receptor, ligand binding	Domain
B, C, E	IPR009167	Erythropoietin receptor	Family
B, C, E	IPR003961	Fibronectin type III	Domain
B, C, E	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, C, E	IPR003528	Long hematopoietin receptor, single chain, conserved site	Conserved Site
B, C, E	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
D, F, H	IPR003597	Immunoglobulin C1-set	Domain
D, F, H	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D, F, H	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D, F, H	IPR013106	Immunoglobulin V-set domain	Domain
D, F, H	IPR003599	Immunoglobulin domain subtype	Domain
D, F, H	IPR007110	Immunoglobulin-like domain	Domain
D, F, H	IPR050380	Immune Recognition and Response Modulators	Family
D, F, H	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, C, E	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