7XTY

Crystal Structure of the second PDZ domain from human PTPN13 in complex with APC peptide

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PDZ domain-like	8038560	3000388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8038560	3000388	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	PF00595	e7xtyA1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PF00595	ECOD (1.6)
B	PF00595	e7xtyB1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PF00595	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF16599	Unstructured linker region on PTN13 protein between PDZ (PTN13_u3)	Unstructured linker region on PTN13 protein between PDZ	-	Disordered
A, B	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain
C, D	PF05937	EB-1 Binding Domain (EB1_binding)	EB-1 Binding Domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Tyrosine-protein phosphatase non-receptor type 13	phosphatidylinositol 3-kinase binding protein binding binding phosphatidylinositol 3-kinase regulatory subunit binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity phosphatase activity hydrolase activity catalytic activity	protein dephosphorylation organonitrogen compound metabolic process dephosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process protein dephosphorylation organonitrogen compound metabolic process dephosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process regulation of cellular process regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process regulation of phosphate metabolic process negative regulation of protein modification process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation regulation of metabolic process cellular response to stimulus cellular response to chemical stimulus response to stimulus response to chemical cellular response to toxic substance response to toxic substance peptidyl-tyrosine dephosphorylation regulation of signaling regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction multicellular organismal process regulation of cellular component organization regulation of developmental process negative regulation of excitatory synapse assembly cellular component organization cellular component biogenesis regulation of nervous system development multicellular organism development cellular component assembly negative regulation of cell junction assembly cell junction assembly regulation of excitatory synapse assembly anatomical structure development regulation of synapse structure or activity negative regulation of nervous system development regulation of multicellular organismal process synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process regulation of multicellular organismal development negative regulation of cellular component organization negative regulation of developmental process nervous system development negative regulation of synapse organization regulation of cellular component biogenesis excitatory synapse assembly regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly negative regulation of multicellular organismal process negative regulation of synapse assembly	cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleolus fibrillar center cell body
C, D	APC-peptide	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity microtubule plus-end binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding gamma-catenin binding cytoskeletal protein binding microtubule binding protein binding binding tubulin binding enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity microtubule plus-end binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding gamma-catenin binding kinase binding protein kinase binding beta-catenin binding protein-containing complex binding dynein complex binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process cellular developmental process cell differentiation cell fate specification cell fate commitment multicellular organism development multicellular organismal process anatomical structure development cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process cellular developmental process cell differentiation cell fate specification cell fate commitment multicellular organism development multicellular organismal process anatomical structure development pattern specification process regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization cell projection organization positive regulation of biological process plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization pseudopodium assembly cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process regulation of biological process plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly biological regulation regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly positive regulation of pseudopodium assembly regulation of pseudopodium assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly pseudopodium organization signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death regulation of microtubule-based process regulation of microtubule-based movement microtubule-based movement microtubule-based process cell migration cell motility bicellular tight junction assembly tight junction organization apical junction assembly cell junction organization cell junction assembly tight junction assembly cell-cell junction assembly cell-cell junction organization nervous system development system development cell adhesion establishment of organelle localization cellular localization attachment of spindle microtubules to kinetochore regulation of cell cycle process establishment of localization metaphase chromosome alignment localization chromosome localization organelle localization establishment of localization in cell nuclear chromosome segregation regulation of attachment of spindle microtubules to kinetochore cell cycle establishment of chromosome localization regulation of cell cycle chromosome segregation cell cycle process protein-containing complex organization protein-containing complex assembly mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division mitotic cell cycle regulation of cell cycle phase transition spindle checkpoint signaling negative regulation of cell cycle regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling mitotic sister chromatid separation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling negative regulation of cellular component organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition regulation of mitotic sister chromatid segregation regulation of chromosome separation negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of mitotic sister chromatid separation regulation of metaphase/anaphase transition of cell cycle spindle assembly checkpoint signaling cell cycle phase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic cell cycle mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition negative regulation of chromosome separation mitotic nuclear division negative regulation of mitotic cell cycle phase transition organelle fission chromosome organization negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling organelle organization nuclear division negative regulation of chromosome segregation chromosome separation negative regulation of organelle organization negative regulation of nuclear division regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition catabolic process positive regulation of protein metabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process organic substance metabolic process positive regulation of macromolecule metabolic process protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process metabolic process macromolecule metabolic process regulation of metabolic process organic substance catabolic process regulation of protein catabolic process regulation of catalytic activity negative regulation of catalytic activity regulation of cyclin-dependent protein kinase activity regulation of transferase activity negative regulation of cellular metabolic process negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process negative regulation of protein modification process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of cyclin-dependent protein serine/threonine kinase activity negative regulation of protein serine/threonine kinase activity negative regulation of macromolecule metabolic process negative regulation of cyclin-dependent protein kinase activity negative regulation of molecular function negative regulation of protein kinase activity regulation of protein kinase activity negative regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of phosphorylation proteolysis involved in protein catabolic process proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process heart development mesenchyme morphogenesis endocardial cushion morphogenesis animal organ development heart morphogenesis mesenchyme development tissue development circulatory system development tissue morphogenesis anatomical structure morphogenesis endocardial cushion development animal organ morphogenesis heart valve development cellular response to nitrogen compound response to organic substance response to peptide hormone insulin receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone cellular response to organic substance enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus response to endogenous stimulus response to organonitrogen compound response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical response to insulin cellular response to insulin stimulus negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition negative regulation of G1/S transition of mitotic cell cycle negative regulation of cell cycle G1/S phase transition regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration locomotion protein localization protein localization to microtubule cytoskeleton regulation of localization regulation of protein localization regulation of protein localization to centrosome protein localization to microtubule organizing center regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to cytoskeleton protein localization to organelle positive regulation of protein localization positive regulation of protein localization to centrosome protein localization to centrosome regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization negative regulation of microtubule depolymerization microtubule cytoskeleton organization protein-containing complex disassembly regulation of protein-containing complex disassembly microtubule polymerization or depolymerization regulation of microtubule depolymerization negative regulation of protein-containing complex disassembly negative regulation of supramolecular fiber organization cellular component disassembly negative regulation of microtubule polymerization or depolymerization regulation of protein depolymerization negative regulation of cytoskeleton organization negative regulation of protein depolymerization microtubule depolymerization regulation of supramolecular fiber organization supramolecular fiber organization protein depolymerization cytoskeleton organization regulation of microtubule cytoskeleton organization regulation of developmental process regulation of cell differentiation	cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasm cytosol cell periphery protein-containing complex extrinsic component of plasma membrane catenin complex plasma membrane protein complex membrane cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasm cytosol cell periphery protein-containing complex extrinsic component of plasma membrane catenin complex plasma membrane protein complex membrane plasma membrane membrane protein complex extrinsic component of membrane cell-cell junction adherens junction anchoring junction cell junction membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system perinuclear region of cytoplasm polymeric cytoskeletal fiber cytoskeleton intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton non-membrane-bounded organelle ruffle leading edge membrane ruffle membrane plasma membrane region cell projection membrane centrosome microtubule organizing center catalytic complex beta-catenin destruction complex intracellular protein-containing complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen Wnt signalosome chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome apical junction complex bicellular tight junction tight junction lateral plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000299	FERM domain	Domain
A, B	IPR014352	FERM/acyl-CoA-binding protein superfamily	Homologous Superfamily
A, B	IPR012153	Tyrosine-protein phosphatase non-receptor type 13	Family
A, B	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A, B	IPR019748	FERM central domain	Domain
A, B	IPR018980	FERM, C-terminal PH-like domain	Domain
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B	IPR019749	Band 4.1 domain	Domain
A, B	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A, B	IPR035963	FERM superfamily, second domain	Homologous Superfamily
A, B	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A, B	IPR036034	PDZ superfamily	Homologous Superfamily
A, B	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A, B	IPR018979	FERM, N-terminal	Domain
A, B	IPR001478	PDZ domain	Domain
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B	IPR011019	KIND domain	Domain
C, D	IPR016024	Armadillo-type fold	Homologous Superfamily
C, D	IPR009240	Adenomatous polyposis coli protein, 15 residue repeat	Repeat
C, D	IPR009232	EB-1 binding	Domain
C, D	IPR000225	Armadillo	Repeat
C, D	IPR009223	Adenomatous polyposis coli protein repeat	Repeat
C, D	IPR026818	Adenomatous polyposis coli (APC) family	Family
C, D	IPR036149	APC, N-terminal coiled-coil domain superfamily	Homologous Superfamily
C, D	IPR009224	SAMP	Repeat
C, D	IPR011989	Armadillo-like helical	Homologous Superfamily
C, D	IPR041257	Adenomatous polyposis coli (APC) repeat	Repeat
C, D	IPR026831	Adenomatous polyposis coli protein	Homologous Superfamily
C, D	IPR009234	Adenomatous polyposis coli protein basic domain	Domain
C, D	IPR032038	Adenomatous polyposis coli, N-terminal dimerisation domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q12923	classic familial adenomatous polyposis glioblastoma lung cancer medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida Crohn disease interstitial cystitis lung carcinoma ovarian cancer peripheral nervous system disease ulcerative colitis cystic fibrosis lung adenocarcinoma malignant mesothelioma classic familial adenomatous polyposis glioblastoma lung cancer medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida Crohn disease interstitial cystitis lung carcinoma ovarian cancer peripheral nervous system disease ulcerative colitis cystic fibrosis lung adenocarcinoma malignant mesothelioma pancreatic intraductal papillary-mucinous carcinoma peripheral neuropathy
C, D	Pharos: P25054	medulloblastoma classic familial adenomatous polyposis glioblastoma colorectal cancer desmoid tumor hepatocellular carcinoma intellectual disability Adenomatous Polyps malignant colon neoplasm mismatch repair cancer syndrome 1 non-small cell lung carcinoma gastric cancer adenoma papillary adenoma follicular thyroid adenoma medulloblastoma classic familial adenomatous polyposis glioblastoma colorectal cancer desmoid tumor hepatocellular carcinoma intellectual disability Adenomatous Polyps malignant colon neoplasm mismatch repair cancer syndrome 1 non-small cell lung carcinoma gastric cancer adenoma papillary adenoma follicular thyroid adenoma Cenani-Lenz syndactyly syndrome giant cell glioblastoma granular cell carcinoma rectal neoplasm adult medulloblastoma microcystic adenoma liver cancer Gardner syndrome Lynch syndrome cancer prostate cancer colorectal adenoma tubular adenocarcinoma medullomyoblastoma with myogenic differentiation intestinal cancer familial adenomatous polyposis 1 benign colon neoplasm macrocytic anemia childhood medulloblastoma hepatoblastoma adenocarcinoma inflammatory bowel disease melanotic medulloblastoma adult acute respiratory distress syndrome liver neoplasm benign mesothelioma malignant glioma psoriasis colorectal adenocarcinoma colorectal carcinoma stomach carcinoma in situ medulloblastoma with extensive nodularity cribriform carcinoma of breast digestive system cancer large cell medulloblastoma attenuated familial adenomatous polyposis ovarian cancer lung adenocarcinoma benign neoplasm of pancreas Pick disease gastric carcinoma colon carcinoma rectal cancer schizophrenia hereditary diffuse gastric adenocarcinoma mammary neoplasms, animal hyperlipidemia adrenal cortex carcinoma desmoplastic/nodular medulloblastoma intestinal polyp digestive system disease atypical teratoid rhabdoid tumor pancreatic neoplasm lung benign neoplasm benign neoplasm of stomach pilocytic astrocytoma primitive neuroectodermal tumor gastric neoplasm genetic intestinal polyposis malignant ependymoma glioma colonic neoplasm rectal carcinoma cribriform carcinoma intestinal neoplasm mesothelioma diabetes mellitus astrocytic tumor exocrine pancreatic carcinoma autism oligodendroglioma familial hyperlipidemia