5JR2

Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	galactose-binding domain-like	8082070	3000087	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8082070	3000087	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	galactose-binding domain-like	8082070	3000087	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	galactose-binding domain-like	8082070	3000087	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	PF01404	e5jr2A1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF01404	ECOD (1.6)
B	PF01404	e5jr2B1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF01404	ECOD (1.6)
C	PF01404	e5jr2C1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF01404	ECOD (1.6)
D	PF01404	e5jr2D1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF01404	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
C	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
D	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	Ephrin type-A receptor 4	molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity amide binding amyloid-beta binding binding peptide binding GPI-linked ephrin receptor activity 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 protein binding DH domain binding protein domain specific binding signaling receptor binding ephrin receptor binding protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding identical protein binding PH domain binding	developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process developmental process ear development sensory organ development inner ear development cochlea development animal organ development anatomical structure development negative regulation of long-term synaptic potentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process negative regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of biological process regulation of signaling biological regulation cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication cellular process positive regulation of signaling adherens junction organization cellular component organization cell junction organization cellular component organization or biogenesis cell-cell junction organization regulation of protein stability protein stabilization cellular response to stimulus cell surface receptor signaling pathway response to stimulus cell surface receptor protein tyrosine kinase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway negative regulation of proteolysis catabolic process negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process macromolecule catabolic process regulation of primary metabolic process organic substance metabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process proteolysis protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process metabolic process macromolecule metabolic process regulation of metabolic process organic substance catabolic process multicellular organismal process cellular developmental process regulation of developmental process astrocyte differentiation regulation of glial cell differentiation regulation of cell differentiation nervous system development regulation of astrocyte differentiation multicellular organism development neurogenesis central nervous system development gliogenesis glial cell differentiation cell differentiation system development negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process positive regulation of metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of cellular metabolic process regulation of molecular function positive regulation of kinase activity regulation of protein tyrosine kinase activity regulation of kinase activity macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of molecular function positive regulation of protein modification process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of protein tyrosine kinase activity regulation of peptidyl-tyrosine phosphorylation positive regulation of catalytic activity regulation of protein kinase activity regulation of phosphorylation peptidyl-tyrosine phosphorylation regulation of neuron projection development regulation of cellular component organization cell projection organization cell development neuron projection development neuron differentiation negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization regulation of cellular response to hypoxia cellular response to oxygen levels cellular response to hypoxia regulation of cellular response to stress cellular response to decreased oxygen levels cellular response to stress regulation of response to stress response to stress response to decreased oxygen levels negative regulation of cellular response to hypoxia cellular response to chemical stimulus response to hypoxia response to chemical response to oxygen levels response to abiotic stimulus protein autophosphorylation plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis anatomical structure morphogenesis neuron projection guidance negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion cell adhesion regulation of epithelial to mesenchymal transition mesenchyme development negative regulation of cell differentiation regulation of multicellular organismal process negative regulation of developmental process tissue development negative regulation of epithelial to mesenchymal transition epithelial to mesenchymal transition mesenchymal cell differentiation negative regulation of multicellular organismal process adult walking behavior adult locomotory behavior behavior adult behavior locomotory behavior walking behavior regulation of hydrolase activity regulation of GTPase activity regulation of cell adhesion negative regulation of cell adhesion neuron projection fasciculation cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of cellular metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance biosynthetic process regulation of biosynthetic process gene expression translation macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process axonogenesis regulation of axonogenesis regulation of anatomical structure morphogenesis axon development cell morphogenesis involved in neuron differentiation regulation of synapse structure or activity dendritic spine morphogenesis synapse organization dendritic spine development dendritic spine organization postsynapse organization regulation of postsynapse organization dendrite development dendrite morphogenesis regulation of synapse organization regulation of dendritic spine morphogenesis neuron projection organization positive regulation of GTP binding regulation of binding regulation of GTP binding positive regulation of binding positive regulation of guanyl-nucleotide exchange factor activity regulation of guanyl-nucleotide exchange factor activity positive regulation of Rho guanyl-nucleotide exchange factor activity motor neuron axon guidance axon guidance amyloid precursor protein catabolic process regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process positive regulation of peptidase activity regulation of amyloid precursor protein catabolic process positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process regulation of aspartic-type peptidase activity regulation of endopeptidase activity amyloid precursor protein metabolic process positive regulation of aspartic-type peptidase activity regulation of peptidase activity positive regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis positive regulation of amyloid precursor protein catabolic process cellular component disassembly regulation of synapse pruning cell junction disassembly synapse pruning regulation of modification of synaptic structure modification of synaptic structure positive regulation of cell adhesion cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation regulation of amide metabolic process regulation of amyloid-beta formation positive regulation of amyloid-beta formation amyloid-beta metabolic process amide metabolic process amyloid-beta formation positive regulation of amide metabolic process negative regulation of neuron projection regeneration regeneration neuron projection regeneration response to wounding regulation of axon regeneration response to external stimulus negative regulation of response to external stimulus regulation of neuron projection regeneration negative regulation of axon regeneration regulation of response to external stimulus response to axon injury regulation of response to wounding axon regeneration negative regulation of response to wounding positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility glial cell migration neuron recognition axonal fasciculation cell recognition fasciculation of sensory neuron axon central nervous system neuron development central nervous system neuron differentiation central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis corticospinal tract morphogenesis cellular response to nitrogen compound response to organic substance response to organonitrogen compound response to endogenous stimulus response to oxygen-containing compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to organonitrogen compound cellular response to organic substance response to amyloid-beta positive regulation of nervous system development regulation of neurogenesis regulation of cell morphogenesis regulation of cell development positive regulation of developmental process regulation of dendrite morphogenesis positive regulation of cell projection organization positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process positive regulation of cellular component organization regulation of nervous system development positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal development positive regulation of dendrite morphogenesis fasciculation of motor neuron axon epithelium development kidney epithelium development nephric duct morphogenesis tube development morphogenesis of an epithelium renal system development tissue morphogenesis tube morphogenesis nephric duct development epithelial tube morphogenesis kidney development	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane cellular anatomical entity postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region somatodendritic compartment cell body perikaryon neuronal cell body presynapse presynaptic membrane cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm glutamatergic synapse cell-cell junction adherens junction anchoring junction neuromuscular junction dendritic shaft neuron spine dendritic spine membrane-bounded organelle mitochondrial membrane mitochondrion organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane axon actin-based cell projection filopodium growth cone distal axon axonal growth cone site of polarized growth cell surface endosome membrane early endosome endosome intracellular vesicle early endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane vesicle Schaffer collateral - CA1 synapse axon terminus neuron projection terminus
E, F, G, H	APYd3 peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001426	Tyrosine-protein kinase, receptor class V, conserved site	Conserved Site
A, B, C, D	IPR034270	Ephrin type-A receptor 4, ligand binding domain	Domain
A, B, C, D	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B, C, D	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR011641	Tyrosine-protein kinase ephrin type A/B receptor-like	Domain
A, B, C, D	IPR016257	Ephrin receptor type-A /type-B	Family
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR001660	Sterile alpha motif domain	Domain
A, B, C, D	IPR001090	Ephrin receptor ligand binding domain	Domain
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR027936	Ephrin receptor, transmembrane domain	Domain
A, B, C, D	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
A, B, C, D	IPR003961	Fibronectin type III	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR030602	Ephrin type-A receptor 4, SAM domain	Domain
A, B, C, D	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P54764	metastatic melanoma pancreatic intraductal papillary-mucinous carcinoma Parkinson disease pilocytic astrocytoma amyotrophic lateral sclerosis atypical teratoid rhabdoid tumor Chronic Myelocytic Leukemia Accelerated Phase cystic fibrosis large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm tuberculosis asthma metastatic melanoma pancreatic intraductal papillary-mucinous carcinoma Parkinson disease pilocytic astrocytoma amyotrophic lateral sclerosis atypical teratoid rhabdoid tumor Chronic Myelocytic Leukemia Accelerated Phase cystic fibrosis large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm tuberculosis asthma glioblastoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia urinary bladder carcinoma astrocytic tumor breast cancer Crohn disease invasive ductal breast carcinoma lung carcinoma malignant mesothelioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F, G, H	BAL
E, F, G, H	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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 R01GM133198.