5MK3 | pdb_00005mk3

Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro 1 domain (CHMP4C peptide complex structure)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Sel1	e5mk3A1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (v294.1)
C	Sel1	e5mk3C1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (v294.1)
D	Sel1	e5mk3D1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (v294.1)
B	Sel1	e5mk3B1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.280	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	alix/aip1 like domains	CATH (4.3.0)
C	1.25.40.280	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	alix/aip1 like domains	CATH (4.3.0)
D	1.25.40.280	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	alix/aip1 like domains	CATH (4.3.0)
B	1.25.40.280	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	alix/aip1 like domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03097	BRO1-like domain (BRO1)	BRO1-like domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Tyrosine-protein phosphatase non-receptor type 23	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 binding binding kinase binding enzyme binding protein kinase binding	adherens junction organization regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization biological regulation positive regulation of biological process cellular component organization regulation of adherens junction organization cell junction organization cellular process cellular component organization or biogenesis positive regulation of cellular process positive regulation of adherens junction organization adherens junction organization regulation of biological process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization biological regulation positive regulation of biological process cellular component organization regulation of adherens junction organization cell junction organization cellular process cellular component organization or biogenesis positive regulation of cellular process positive regulation of adherens junction organization cell-cell junction organization catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process positive regulation of homophilic cell adhesion homophilic cell-cell adhesion regulation of homophilic cell adhesion positive regulation of cell adhesion regulation of cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis organelle organization cellular component assembly cilium assembly cilium organization cell projection assembly positive regulation of cell communication regulation of localization establishment of protein localization regulation of protein localization signaling transport positive regulation of establishment of protein localization positive regulation of secretion by cell cell communication protein localization to extracellular region positive regulation of protein transport localization secretion by cell regulation of secretion by cell positive regulation of secretion signal release intracellular protein localization regulation of Wnt protein secretion regulation of signaling secretion regulation of transport positive regulation of Wnt protein secretion establishment of protein localization to extracellular region regulation of establishment of protein localization cell-cell signaling export from cell regulation of protein transport Wnt protein secretion protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport macromolecule localization positive regulation of protein localization regulation of cell communication positive regulation of signaling multicellular organismal process negative regulation of locomotion regulation of cell motility negative regulation of biological process tissue migration negative regulation of epithelial cell migration ameboidal-type cell migration regulation of cell migration negative regulation of cellular process regulation of multicellular organismal process cell migration epithelial cell migration cell motility regulation of epithelial cell migration locomotion negative regulation of cell migration epithelium migration regulation of locomotion negative regulation of cell motility negative regulation of multicellular organismal process cellular localization establishment of protein localization to vacuole vesicle-mediated transport late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway establishment of localization in cell endosome transport via multivesicular body sorting pathway protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway protein localization to vacuole intracellular transport endosomal transport establishment of protein localization to organelle multivesicular body sorting pathway protein localization to organelle vacuolar transport intracellular protein transport positive regulation of early endosome to late endosome transport positive regulation of intracellular transport regulation of intracellular transport regulation of vesicle-mediated transport vesicle-mediated transport between endosomal compartments regulation of early endosome to late endosome transport early endosome to late endosome transport regulation of cellular localization localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular membraneless organelle intracellular organelle centrosome extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular membraneless organelle intracellular organelle centrosome microtubule organizing center cytoskeleton centriolar satellite membraneless organelle microtubule cytoskeleton cytoplasm cytosol cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cell periphery external encapsulating structure glycocalyx sperm glycocalyx early endosome endosome intracellular vesicle endomembrane system cytoplasmic vesicle nuclear body ciliary basal body
E, F, G, H	Charged multivesicular body protein 4c	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway establishment of localization in cell cellular process vacuolar transport endosome transport via multivesicular body sorting pathway cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway establishment of localization in cell cellular process vacuolar transport endosome transport via multivesicular body sorting pathway membrane fusion organelle membrane fusion endosome to lysosome transport lysosomal transport multivesicular body-lysosome fusion cellular component organization vesicle organization endosome to lysosome transport via multivesicular body sorting pathway lysosome organization cellular component organization or biogenesis membrane organization vacuole organization lytic vacuole organization lysosomal membrane organization organelle fusion organelle organization vesicle fusion regulation of cytokinesis regulation of biological process regulation of cellular process negative regulation of cytokinesis regulation of cell cycle process biological regulation negative regulation of biological process negative regulation of cell cycle cytokinesis negative regulation of cell cycle process regulation of cell division negative regulation of cell division negative regulation of cellular process cell cycle cell division regulation of cell cycle cell cycle process cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism membrane biogenesis nuclear membrane reassembly membrane assembly nuclear membrane organization cellular component biogenesis nucleus organization cellular component assembly nuclear envelope organization endomembrane system organization organelle assembly multivesicular body assembly multivesicular body organization endosome organization cellular response to stimulus regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle negative regulation of cell cycle phase transition signal transduction mitotic cytokinesis checkpoint signaling cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition establishment of protein localization protein transport macromolecule localization intracellular protein localization primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process protein metabolic process macromolecule metabolic process mitotic nuclear division mitotic metaphase chromosome alignment organelle fission chromosome organization sister chromatid segregation metaphase chromosome alignment nuclear division chromosome localization organelle localization nuclear chromosome segregation mitotic sister chromatid segregation chromosome segregation regulation of cytoskeleton organization regulation of cellular component organization microtubule cytoskeleton organization regulation of mitotic spindle organization membraneless organelle assembly regulation of mitotic spindle assembly microtubule cytoskeleton organization involved in mitosis spindle organization regulation of microtubule-based process regulation of spindle organization regulation of cellular component biogenesis spindle assembly regulation of organelle organization mitotic spindle organization regulation of spindle assembly mitotic spindle assembly regulation of organelle assembly microtubule-based process cytoskeleton organization regulation of microtubule cytoskeleton organization microtubule organizing center organization regulation of centrosome cycle centrosome duplication centrosome cycle regulation of centrosome duplication cytoskeleton-dependent cytokinesis mitotic cytokinetic process mitotic cytokinesis midbody abscission cytokinetic process ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway virion assembly viral process viral budding viral budding via host ESCRT complex viral life cycle vesicle budding from membrane membrane fission biological process involved in interspecies interaction between organisms non-lytic viral release biological process involved in interaction with host biological process involved in symbiotic interaction exit from host cell viral budding from plasma membrane viral release from host cell late endosome to lysosome transport wound healing plasma membrane repair response to stress plasma membrane organization response to wounding vesicle fusion with vacuole vacuole fusion	midbody cellular anatomical structure membrane-bounded organelle endosome membrane intracellular anatomical structure endosome membrane multivesicular body membrane intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane midbody cellular anatomical structure membrane-bounded organelle endosome membrane intracellular anatomical structure endosome membrane multivesicular body membrane intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome cytoplasm vesicle organelle membrane multivesicular body cytosol protein-containing complex ESCRT complex membrane protein complex ESCRT III complex cell periphery plasma membrane vacuolar membrane autophagosome membrane vacuole autophagosome amphisome membrane amphisome nucleus nuclear protein-containing complex organelle envelope nuclear envelope nuclear pore polymeric cytoskeletal fiber spindle intracellular membraneless organelle spindle microtubule kinetochore microtubule cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton lytic vacuole lytic vacuole membrane lysosomal membrane lysosome chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome Flemming body cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004328	BRO1 domain	Domain
A, B, C, D	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A, B, C, D	IPR025304	ALIX V-shaped domain	Domain
A, B, C, D	IPR038499	BRO1 domain superfamily	Homologous Superfamily
A, B, C, D	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A, B, C, D	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A, B, C, D	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A, B, C, D	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
E, F, G, H	IPR005024	Snf7 family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9H3S7	epilepsy microcephaly Epileptic encephalopathy osteosarcoma intellectual disability
E, F, G, H	Pharos: Q96CF2	ovarian cancer atopic eczema Malignant neoplasm of ovary ovarian neoplasm interstitial cystitis spina bifida invasive ductal breast carcinoma ovarian carcinoma X-linked mixed deafness with perilymphatic gusher

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.