6N5Z | pdb_00006n5z

Crystal structure of the SNX5 PX domain in complex with the Sema4C

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)
B	SCOP2B Superfamily	PX domain	8100750	3001006	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PX domain	8100750	3001006	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)
B	V-set	e6n5zB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: V-set	ECOD (v294.1)
A	MAM33	e6n5zA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MAM33	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	CATH (utative)
A	3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00787	PX domain (PX)	PX domain	PX domains bind to phosphoinositides.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Sorting nexin-5,Semaphorin-4C	protein binding binding signaling receptor binding neuropilin binding semaphorin receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity chemorepellent activity receptor ligand activity signaling receptor activator activity ion binding anion binding phosphatidylinositol binding protein binding binding signaling receptor binding neuropilin binding semaphorin receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity chemorepellent activity receptor ligand activity signaling receptor activator activity ion binding anion binding phosphatidylinositol binding small molecule binding phosphatidylinositol-3,5-bisphosphate binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding cell adhesion molecule binding cadherin binding phosphatidylinositol-4-phosphate binding phosphatidylinositol-5-phosphate binding D1 dopamine receptor binding G protein-coupled receptor binding dopamine receptor binding cytoskeletal protein binding dynactin binding	developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development cell migration cellular process cell motility hindbrain development cell migration in hindbrain developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development cell migration cellular process cell motility hindbrain development cell migration in hindbrain system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of cellular response to stress positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus stress-activated MAPK cascade cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress intracellular signaling cassette signal transduction positive regulation of stress-activated protein kinase signaling cascade positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of stress-activated MAPK cascade positive regulation of MAPK cascade biological regulation regulation of stress-activated protein kinase signaling cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling cerebellum development metencephalon development stem cell development neural crest cell differentiation cellular developmental process neural crest cell development cell development mesenchyme development tissue development mesenchymal cell migration stem cell differentiation cell differentiation ameboidal-type cell migration mesenchymal cell differentiation neural crest cell migration embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure cell surface receptor signaling pathway semaphorin-plexin signaling pathway regulation of cellular component organization cellular component organization cellular component biogenesis cellular component assembly regulation of postsynapse assembly cell junction assembly regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality postsynapse organization postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly chemotaxis negative chemotaxis taxis response to chemical response to external stimulus locomotion axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development 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 muscle structure development muscle cell differentiation catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy regulation of macroautophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway regulation of cellular response to insulin stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus positive regulation of cellular response to insulin stimulus response to endogenous stimulus regulation of insulin receptor signaling pathway positive regulation of insulin receptor signaling pathway 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 response to insulin cellular response to insulin stimulus vesicle-mediated transport endosomal transport intercellular transport cytosolic transport retrograde transport, endosome to Golgi positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription negative regulation of signaling negative regulation of ERBB signaling pathway negative regulation of biological process macromolecule catabolic process negative regulation of cell communication regulation of epidermal growth factor receptor signaling pathway negative regulation of cellular process epidermal growth factor receptor signaling pathway epidermal growth factor catabolic process protein metabolic process regulation of ERBB signaling pathway negative regulation of response to stimulus protein catabolic process negative regulation of signal transduction negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway import into cell pinocytosis endocytosis system process circulatory system process regulation of blood pressure negative regulation of blood pressure blood circulation	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region glutamatergic synapse membrane-bounded organelle intracellular anatomical structure intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle presynapse bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane secretory vesicle cytoplasm organelle membrane exocytic vesicle cell projection macropinocytic cup plasma membrane bounded cell projection protein-containing complex membrane protein complex retromer complex cytosol apical part of cell cluster of actin-based cell projections brush border retromer, tubulation complex endosome membrane cytoplasmic side of membrane early endosome early endosome membrane cytoplasmic side of endosome membrane cytoplasmic side of early endosome membrane endosome side of membrane tubular endosome ruffle cell leading edge perinuclear region of cytoplasm phagocytic cup cytoplasmic side of plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR016201	PSI domain	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR027231	Semaphorin	Family
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B	IPR002165	Plexin repeat	Repeat
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR001627	Sema domain	Domain
A, B	IPR014637	Sorting nexin-5/6/32	Family
A, B	IPR042135	SNX5, PX domain	Domain
A, B	IPR001683	Phox homology	Domain
A, B	IPR028654	Sorting nexin-5, BAR domain	Domain
A, B	IPR027267	AH/BAR domain superfamily	Homologous Superfamily
A, B	IPR015404	Sorting nexin/Vps5-like, C-terminal	Domain
A, B	IPR036871	PX domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9Y5X3	malignant mesothelioma psoriasis osteosarcoma subependymal giant cell astrocytoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor Disease Exacerbation gastric carcinoma hereditary diffuse gastric adenocarcinoma malignant ependymoma medulloblastoma pancreatic ductal adenocarcinoma Sjogren syndrome breast cancer malignant mesothelioma psoriasis osteosarcoma subependymal giant cell astrocytoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor Disease Exacerbation gastric carcinoma hereditary diffuse gastric adenocarcinoma malignant ependymoma medulloblastoma pancreatic ductal adenocarcinoma Sjogren syndrome breast cancer gastric neoplasm invasive ductal breast carcinoma malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma cystic fibrosis gastric cancer Hashimoto thyroiditis large cell medulloblastoma ovarian cancer

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.