3SKJ

Structural And Functional Characterization of an Agonistic Anti-Human EphA2 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
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 [auth L]	d3skjl2	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 [auth L]	d3skjl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth M]	d3skjm2	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)
C [auth M]	d3skjm1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d3skjh_	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)
D [auth I]	d3skji_	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)
E	d3skje_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	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)
E	SCOP2 Family	Ephrin receptor ligand binding domain	8082077	4002471	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	galactose-binding domain-like	8082078	3000087	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)
A [auth L]	C1-set_4	e3skjL2	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 [auth L]	V-set	e3skjL1	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)
C [auth M]	C1-set_4	e3skjM2	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)
C [auth M]	V-set	e3skjM1	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 [auth H]	C1-set_1	e3skjH2	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)
B [auth H]	V-set_12	e3skjH1	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)
D [auth I]	C1-set_1	e3skjI2	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)
D [auth I]	V-set_12	e3skjI1	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)
E	Ephrin_lbd	e3skjE1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Ephrin_lbd	ECOD (1.6)
F	Ephrin_lbd	e3skjF2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Ephrin_lbd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
F	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	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 [auth L], C [auth M]	Fab anti-human EphA2	L-KAPPA	Homo sapiens (human)	IGKV1-503, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)
B [auth H], D [auth I]	Fab anti-human EphA2	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHJ101, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L], C [auth M]	Light Chain	IGKV1	Kappa	ephrin type-a receptor 2	SAbDab (2024-11-15)
B [auth H], D [auth I]	Heavy Chain	IGHV3	-	ephrin type-a receptor 2	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F	PF01404	Ephrin receptor ligand binding domain (Ephrin_lbd)	Ephrin receptor ligand binding domain	The Eph receptors, which bind to ephrins Pfam:PF00812 are a large family of receptor tyrosine kinases. This family represents the amino terminal domain which binds the ephrin ligand [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L], C [auth M]	Antibody, light chain	-	-	-
B [auth H], D [auth I]	Antibody, heavy chain	-	-	-
E, F	Ephrin type-A receptor 2	molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity binding molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ephrin receptor activity cell adhesion molecule binding cadherin binding protein binding virus receptor activity exogenous protein binding growth factor binding molecular function activator activity molecular function regulator activity	developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis regulation of angiogenesis anatomical structure development anatomical structure formation involved in morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development skeletal system development positive regulation of protein localization to plasma membrane protein localization regulation of localization cellular localization regulation of cellular process regulation of protein localization positive regulation of biological process localization cellular macromolecule localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane localization within membrane regulation of protein localization to cell periphery protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process regulation of protein localization to plasma membrane cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway cell migration cell motility cellular developmental process animal organ development cell development notochord cell development embryo development cell differentiation embryonic organ development notochord development notochord cell differentiation negative regulation of biological process negative regulation of chemokine production regulation of cytokine production cytokine production negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of chemokine production regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process chemokine production regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process post-anal tail morphogenesis lymphangiogenesis negative regulation of developmental process regulation of lymphangiogenesis negative regulation of lymphangiogenesis lymph vessel morphogenesis lymph vessel development regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration blood vessel endothelial cell migration locomotion cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical sensory organ development visual system development cell morphogenesis epithelial cell differentiation eye morphogenesis lens morphogenesis in camera-type eye animal organ morphogenesis sensory system development camera-type eye morphogenesis lens fiber cell morphogenesis epithelium development eye development tissue development lens fiber cell development epithelial cell development sensory organ morphogenesis camera-type eye development lens fiber cell differentiation lens development in camera-type eye regulation of signaling regulation of signal transduction regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade cell adhesion cell population proliferation blood vessel endothelial cell proliferation involved in sprouting angiogenesis endothelial cell proliferation sprouting angiogenesis epithelial cell proliferation branching involved in mammary gland duct morphogenesis mammary gland morphogenesis mammary gland development branching morphogenesis of an epithelial tube gland development gland morphogenesis epithelial tube morphogenesis morphogenesis of an epithelium mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development morphogenesis of a branching structure morphogenesis of a branching epithelium nucleoside phosphate metabolic process ribose phosphate metabolic process cAMP metabolic process cyclic purine nucleotide metabolic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process cyclic nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process purine ribonucleotide metabolic process phosphorus metabolic process tissue remodeling bone remodeling embryonic organ morphogenesis embryonic morphogenesis notochord morphogenesis notochord formation nervous system development ossification osteoblast differentiation epidermal cell differentiation epidermis development skin development keratinocyte differentiation cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion pericyte cell differentiation formation of primary germ layer mesoderm morphogenesis gastrulation axial mesoderm development axial mesoderm formation axial mesoderm morphogenesis mesoderm formation mesoderm development generation of neurons neurogenesis neuron differentiation mammary gland epithelial cell proliferation cell death apoptotic signaling pathway cellular response to stress DNA damage response response to stress intrinsic apoptotic signaling pathway in response to DNA damage apoptotic process intrinsic apoptotic signaling pathway programmed cell death vasculogenesis positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility response to endogenous stimulus response to growth factor myeloid leukocyte differentiation hemopoiesis myeloid cell differentiation osteoclast differentiation leukocyte differentiation activation of GTPase activity positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity defense response inflammatory response neural tube development chordate embryonic development embryo development ending in birth or egg hatching lamellipodium assembly regulation of cellular component organization plasma membrane bounded cell projection organization cell projection organization regulation of cell projection organization regulation of cell projection assembly plasma membrane bounded cell projection assembly regulation of cellular component biogenesis cellular component organization cellular component biogenesis regulation of plasma membrane bounded cell projection assembly regulation of lamellipodium assembly cellular component assembly regulation of lamellipodium organization lamellipodium organization cellular component organization or biogenesis regulation of plasma membrane bounded cell projection organization cell projection assembly negative regulation of blood vessel morphogenesis negative regulation of angiogenesis negative regulation of vasculature development bicellular tight junction assembly positive regulation of cellular component organization tight junction organization cell junction assembly cell-cell junction assembly cell-cell junction organization regulation of bicellular tight junction assembly positive regulation of cellular component biogenesis apical junction assembly regulation of cell junction assembly positive regulation of cell junction assembly positive regulation of bicellular tight junction assembly cell junction organization tight junction assembly biological process involved in interspecies interaction between organisms response to other organism defense response to Gram-positive bacterium response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium response to external biotic stimulus	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium protein-containing complex receptor complex anchoring junction cell junction focal adhesion cell-substrate junction ruffle plasma membrane membrane cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium protein-containing complex receptor complex anchoring junction cell junction focal adhesion cell-substrate junction ruffle plasma membrane membrane leading edge membrane cell periphery ruffle membrane plasma membrane region cell projection membrane cell surface lamellipodium membrane cell-cell junction tight junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR001426	Tyrosine-protein kinase, receptor class V, conserved site	Conserved Site
E, F	IPR008266	Tyrosine-protein kinase, active site	Active Site
E, F	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
E, F	IPR000719	Protein kinase domain	Domain
E, F	IPR016257	Ephrin receptor type-A /type-B	Family
E, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E, F	IPR001660	Sterile alpha motif domain	Domain
E, F	IPR001090	Ephrin receptor ligand binding domain	Domain
E, F	IPR034263	Ephrin type-A receptor 2, ligand binding domain	Domain
E, F	IPR017441	Protein kinase, ATP binding site	Binding Site
E, F	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
E, F	IPR027936	Ephrin receptor, transmembrane domain	Domain
E, F	IPR050449	Ephrin receptor tyrosine kinases	Family
E, F	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
E, F	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
E, F	IPR003961	Fibronectin type III	Domain
E, F	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
E, F	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
E, F	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F	Pharos: P29317	Noonan syndrome cancer Noonan syndrome with multiple lentigines cataract 6 multiple types cataract nasopharyngeal carcinoma Nuclear non-senile cataract pancreatic intraductal papillary-mucinous neoplasm adrenal cortex carcinoma benign neoplasm sarcoidosis squamous cell lung carcinoma malignant pancreatic neoplasm ovarian cancer atopic eczema Noonan syndrome cancer Noonan syndrome with multiple lentigines cataract 6 multiple types cataract nasopharyngeal carcinoma Nuclear non-senile cataract pancreatic intraductal papillary-mucinous neoplasm adrenal cortex carcinoma benign neoplasm sarcoidosis squamous cell lung carcinoma malignant pancreatic neoplasm ovarian cancer atopic eczema sinusitis gastric adenocarcinoma medulloblastoma non-alcoholic fatty liver disease nuclear cataract pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor psoriasis breast cancer spina bifida ulcerative colitis lung carcinoma

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.