5IXF | pdb_00005ixf

Solution structure of the STAM2 SH3 with AMSH derived peptide complex

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SH3-domain	8062102	4000369	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SH3-domain	8062103	3000153	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		e5ixfA1	A: Long alpha-hairpin	X: Ribosomal protein L29 (L29p)	H: Ribosomal protein L29 (L29p)	T: Lectin_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00018	SH3 domain (SH3_1)	SH3 domain	SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	STAM-binding protein	protein binding binding protein domain specific binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity metal-dependent deubiquitinase activity metallopeptidase activity K63-linked deubiquitinase activity cation binding ion binding protein binding binding protein domain specific binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity metal-dependent deubiquitinase activity metallopeptidase activity K63-linked deubiquitinase activity cation binding ion binding metal ion binding small molecule binding	neuron apoptotic process hippocampal neuron apoptotic process cellular process apoptotic process cell death programmed cell death mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division cell cycle mitotic cell cycle cell cycle process neuron apoptotic process hippocampal neuron apoptotic process cellular process apoptotic process cell death programmed cell death mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division cell cycle mitotic cell cycle cell cycle process cellular response to stimulus regulation of cellular process small GTPase-mediated signal transduction response to stimulus signaling negative regulation of signaling regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction regulation of Ras protein signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus Ras protein signal transduction negative regulation of small GTPase mediated signal transduction biological regulation negative regulation of signal transduction negative regulation of Ras protein signal transduction regulation of response to stimulus regulation of cell communication protein deubiquitination protein K63-linked deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway cell surface receptor signaling pathway via JAK-STAT regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death regulation of hippocampal neuron apoptotic process negative regulation of apoptotic process negative regulation of hippocampal neuron apoptotic process regulation of neuron apoptotic process proteolysis	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 cytoplasm cytosol cell periphery 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 cytoplasm cytosol cell periphery plasma membrane membrane cell division site cleavage furrow plasma membrane region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen early endosome endosome intracellular vesicle endomembrane system cytoplasmic vesicle
A	Signal transducing adapter molecule 2	binding phospholipid binding lipid binding phosphatidylinositol binding protein binding ubiquitin binding ubiquitin-like protein binding	membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly vesicle organization cellular component biogenesis membrane organization cellular component organization membrane fission cellular process cellular component organization or biogenesis catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism organelle assembly multivesicular body assembly vesicle organization cellular component biogenesis organelle organization cellular component assembly multivesicular body organization endosome organization endomembrane system organization establishment of protein localization cellular localization transport establishment of protein localization to vacuole macromolecule catabolic process vesicle-mediated transport localization late endosome to vacuole transport modification-dependent macromolecule catabolic process late endosome to vacuole transport via multivesicular body sorting pathway establishment of localization in cell protein metabolic process intracellular protein localization endosome transport via multivesicular body sorting pathway protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway primary metabolic process protein localization to vacuole intracellular transport protein catabolic process establishment of localization endosomal transport establishment of protein localization to organelle protein transport modification-dependent protein catabolic process multivesicular body sorting pathway protein localization to organelle macromolecule localization ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process vacuolar transport macromolecule metabolic process intracellular protein transport cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction cell communication	membrane-bounded organelle endosome membrane intracellular anatomical structure early endosome endosome membrane intracellular vesicle early endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle membrane-bounded organelle endosome membrane intracellular anatomical structure early endosome endosome membrane intracellular vesicle early endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle cytoplasm vesicle organelle membrane ESCRT-0 complex protein-containing complex ESCRT complex cytosol endocytic vesicle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR044098	STAMBP/STALP-like, MPN domain	Domain
B	IPR015063	USP8 dimerisation domain	Domain
B	IPR037518	MPN domain	Domain
B	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain
A	IPR035675	STAM2, SH3 domain	Domain
A	IPR002014	VHS domain	Domain
A	IPR008942	ENTH/VHS	Homologous Superfamily
A	IPR050670	Signal Transducing Adapter Molecule	Family
A	IPR001452	SH3 domain	Domain
A	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A	IPR003903	Ubiquitin interacting motif	Conserved Site
A	IPR047493	STAM2, VHS domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: O95630	microcephaly-capillary malformation syndrome microcephaly brain disease epilepsy osteosarcoma Severe Congenital Microcephaly cerebrovascular disorder intellectual disability ovarian cancer developmental disability malignant glioma microlissencephaly capillary malformation-arteriovenous malformation syndrome glioblastoma
A	Pharos: O75886	adenoma glioblastoma malignant mesothelioma ovarian cancer alopecia hepatocellular carcinoma non-small cell lung carcinoma psoriasis cardiovascular disease large cell medulloblastoma osteosarcoma tuberculosis

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.