5EMB | pdb_00005emb

Crystal structure of the SNX27 PDZ domain bound to the C-terminal phosphorylated PTHR PDZ binding motif

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PDZ domain-like	8062276	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	PDZ	e5embA1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	GLU-GLU-TRP-SEP-THR-VAL-MET	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity amide binding peptide hormone binding hormone binding peptide receptor activity molecular transducer activity G protein-coupled receptor activity G protein-coupled peptide receptor activity signaling receptor activity transmembrane signaling receptor activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity amide binding peptide hormone binding hormone binding peptide receptor activity molecular transducer activity G protein-coupled receptor activity G protein-coupled peptide receptor activity signaling receptor activity transmembrane signaling receptor activity parathyroid hormone receptor activity	developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development multicellular organism development skeletal system development system development cell population proliferation cellular process cellular response to stimulus developmental process multicellular organismal process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development multicellular organism development skeletal system development system development cell population proliferation cellular process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis osteoblast development cellular developmental process cell differentiation cell development osteoblast differentiation embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development anatomical structure maturation cell maturation developmental maturation adenylate cyclase-activating G protein-coupled receptor signaling pathway 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 negative regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process phospholipase C-activating G protein-coupled receptor signaling pathway connective tissue development chondrocyte differentiation cartilage development regulation of inositol phosphate biosynthetic process alcohol metabolic process positive regulation of phosphate metabolic process inositol phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process phosphate-containing compound metabolic process polyol biosynthetic process small molecule metabolic process phosphorus metabolic process regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process polyol metabolic process positive regulation of phosphorus metabolic process regulation of alcohol biosynthetic process small molecule biosynthetic process carbohydrate biosynthetic process primary metabolic process positive regulation of inositol phosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process inositol phosphate biosynthetic process alcohol biosynthetic process metabolic process regulation of phosphorus metabolic process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process regulation of metabolic process positive regulation of alcohol biosynthetic process multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane cytoplasm cytosol basal part of cell basal plasma membrane basolateral plasma membrane protein-containing complex receptor complex
A	Sorting nexin-27	binding phospholipid binding lipid binding phosphatidylinositol binding ionotropic glutamate receptor binding protein binding signaling receptor binding glutamate receptor binding calcium-dependent protein binding phosphatidylinositol-3-phosphate binding phosphatidylinositol phosphate binding	positive regulation of AMPA glutamate receptor clustering regulation of localization regulation of postsynaptic membrane organization cellular localization positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization regulation of protein localization regulation of AMPA glutamate receptor clustering positive regulation of postsynaptic membrane organization positive regulation of biological process cellular component organization localization receptor clustering positive regulation of AMPA glutamate receptor clustering regulation of localization regulation of postsynaptic membrane organization cellular localization positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization regulation of protein localization regulation of AMPA glutamate receptor clustering positive regulation of postsynaptic membrane organization positive regulation of biological process cellular component organization localization receptor clustering cellular component organization or biogenesis synapse organization intracellular protein localization regulation of receptor clustering postsynaptic membrane organization regulation of protein localization to membrane positive regulation of cellular process membrane organization regulation of biological process postsynapse organization positive regulation of receptor clustering AMPA glutamate receptor clustering biological regulation positive regulation of protein localization to membrane glutamate receptor clustering neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane regulation of glutamate receptor clustering cell junction organization regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process regulation of postsynaptic membrane neurotransmitter receptor levels regulation of biological quality transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport establishment of localization in cell vacuolar transport protein localization to cell periphery establishment of protein localization nitrogen compound transport neurotransmitter receptor transport establishment of protein localization to membrane protein-containing complex localization vesicle-mediated transport to the plasma membrane neurotransmitter receptor transport to plasma membrane protein transport cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor cellular response to stimulus signaling signal transduction cell communication intracellular protein transport developmental process multicellular organismal process regulation of developmental process nervous system development developmental maturation synapse maturation regulation of synapse organization multicellular organism development regulation of synapse maturation anatomical structure development regulation of synapse structure or activity system development endosomal transport response to amine response to methamphetamine hydrochloride response to chemical response to nitrogen compound establishment of protein localization to plasma membrane endocytic recycling protein localization to plasma membrane endosome to plasma membrane protein transport	protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system intracellular anatomical structure WASH complex cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system intracellular anatomical structure WASH complex cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle vesicle cell periphery immunological synapse plasma membrane postsynaptic recycling endosome recycling endosome postsynaptic endosome postsynapse postsynaptic early endosome endosome membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane Schaffer collateral - CA1 synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR017983	GPCR, family 2, secretin-like, conserved site	Conserved Site
B	IPR050332	G-protein coupled receptor 2	Family
B	IPR036445	GPCR family 2, extracellular hormone receptor domain superfamily	Homologous Superfamily
B	IPR002170	GPCR, family 2, parathyroid hormone receptor	Family
B	IPR000832	GPCR, family 2, secretin-like	Family
B	IPR017981	GPCR, family 2-like, 7TM	Domain
B	IPR001879	GPCR, family 2, extracellular hormone receptor domain	Domain
A	IPR037835	SNX27, RA domain	Domain
A	IPR001683	Phox homology	Domain
A	IPR000159	Ras-associating domain	Domain
A	IPR037827	SNX27, atypical FERM-like domain	Domain
A	IPR037833	SNX27, PX domain	Domain
A	IPR036034	PDZ superfamily	Homologous Superfamily
A	IPR036871	PX domain superfamily	Homologous Superfamily
A	IPR001478	PDZ domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q03431	Eiken syndrome metaphyseal chondrodysplasia, Jansen type rickets chondrodysplasia Blomstrand type Ollier disease primary failure of tooth eruption hyperparathyroidism medulloblastoma osteogenesis imperfecta psoriasis adrenal cortex adenoma breast carcinoma Glucocorticoid Induced Osteoporosis large cell medulloblastoma malignant glioma Eiken syndrome metaphyseal chondrodysplasia, Jansen type rickets chondrodysplasia Blomstrand type Ollier disease primary failure of tooth eruption hyperparathyroidism medulloblastoma osteogenesis imperfecta psoriasis adrenal cortex adenoma breast carcinoma Glucocorticoid Induced Osteoporosis large cell medulloblastoma malignant glioma postmenopausal osteoporosis adrenal cortex carcinoma hepatocellular carcinoma hypoparathyroidism lung disease malignant mesothelioma tooth ankylosis glioblastoma intellectual disability

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.