2YD5 | pdb_00002yd5

Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase LAR

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d2yd5a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	VEGFR-1-like_Ig-like	e2yd5A3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: VEGFR-1-like_Ig-like	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07679	Immunoglobulin I-set domain (I-set)	Immunoglobulin I-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F	phosphoric ester hydrolase activity molecular transducer activity catalytic activity, acting on a protein phosphatase activity signaling receptor activity hydrolase activity phosphoprotein phosphatase activity hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity transmembrane receptor protein phosphatase activity transmembrane signaling receptor activity transmembrane receptor protein tyrosine phosphatase activity catalytic activity cell adhesion molecule binding phosphoric ester hydrolase activity molecular transducer activity catalytic activity, acting on a protein phosphatase activity signaling receptor activity hydrolase activity phosphoprotein phosphatase activity hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity transmembrane receptor protein phosphatase activity transmembrane signaling receptor activity transmembrane receptor protein tyrosine phosphatase activity catalytic activity cell adhesion molecule binding protein binding binding proteoglycan binding chondroitin sulfate proteoglycan binding carbohydrate derivative binding protein-containing complex binding heparin binding glycosaminoglycan binding sulfur compound binding	cellular component organization cell adhesion cell junction organization cell-cell adhesion cellular process synaptic membrane adhesion synapse organization cellular component organization or biogenesis cell migration cell motility cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus cellular component organization cell adhesion cell junction organization cell-cell adhesion cellular process synaptic membrane adhesion synapse organization cellular component organization or biogenesis cell migration cell motility cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction cell communication negative regulation of receptor binding regulation of protein binding regulation of molecular function regulation of receptor binding negative regulation of protein binding regulation of binding negative regulation of binding negative regulation of molecular function developmental process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development protein dephosphorylation dephosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process peptidyl-tyrosine dephosphorylation cell surface receptor signaling pathway cell surface receptor protein tyrosine phosphatase signaling pathway enzyme-linked receptor protein signaling pathway regulation of neuron projection development regulation of cellular component organization regulation of developmental process cellular developmental process regulation of response to external stimulus cell projection organization regulation of cellular response to stress cell development neuron projection development regeneration response to axon injury neuron projection regeneration regulation of response to wounding neurogenesis cellular response to stress neuron differentiation axon regeneration regulation of response to stress response to stress cell differentiation response to wounding regulation of axon regeneration plasma membrane bounded cell projection organization regulation of cell projection organization response to external stimulus axon development generation of neurons regulation of response to stimulus neuron development regulation of neuron projection regeneration regulation of plasma membrane bounded cell projection organization	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane cell projection neuron projection extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane cell projection neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR003598	Immunoglobulin subtype 2	Domain
A	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A	IPR003599	Immunoglobulin domain subtype	Domain
A	IPR013098	Immunoglobulin I-set	Domain
A	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A	IPR050713	Receptor-type Tyrosine-protein Phosphatases/Ushers	Family
A	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A	IPR003961	Fibronectin type III	Domain
A	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P10586	breasts and/or nipples, aplasia or hypoplasia of, 2 malignant mesothelioma Malignant neoplasm of stomach non-small cell lung carcinoma psoriasis adrenal cortex carcinoma autism spectrum disorder endogenous depression hereditary diffuse gastric adenocarcinoma lung cancer medulloblastoma ovarian cancer ulcerative colitis astrocytic tumor bipolar disorder breasts and/or nipples, aplasia or hypoplasia of, 2 malignant mesothelioma Malignant neoplasm of stomach non-small cell lung carcinoma psoriasis adrenal cortex carcinoma autism spectrum disorder endogenous depression hereditary diffuse gastric adenocarcinoma lung cancer medulloblastoma ovarian cancer ulcerative colitis astrocytic tumor bipolar disorder cutaneous lupus erythematosus gastric cancer interstitial cystitis myopathy pancreatic intraductal papillary-mucinous carcinoma attention deficit hyperactivity disorder, inattentive type cystic fibrosis Emery-Dreifuss muscular dystrophy gastric neoplasm lung adenocarcinoma

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.