5L7K | pdb_00005l7k

The crystal structure of myristoylated NPHP3 peptide in complex with UNC119a

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)
C [auth G]	GMP_PDE_delta	e5l7kG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GMP_PDE_delta	ECOD (1.6)
A	GMP_PDE_delta	e5l7kA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GMP_PDE_delta	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth G]	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
A	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth G]	PF05351	GMP-PDE, delta subunit (GMP_PDE_delta)	GMP-PDE, delta subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	GLY-THR-ALA-SER-SER-LEU	-	developmental process multicellular organismal process gland development animal organ development pattern specification process liver development regionalization determination of liver left/right asymmetry multicellular organism development hepaticobiliary system development determination of bilateral symmetry anatomical structure development determination of left/right symmetry left/right pattern formation developmental process multicellular organismal process gland development animal organ development pattern specification process liver development regionalization determination of liver left/right asymmetry multicellular organism development hepaticobiliary system development determination of bilateral symmetry anatomical structure development determination of left/right symmetry left/right pattern formation system development specification of symmetry cellular component organization extracellular matrix organization cellular process cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization cellular response to stimulus regulation of cellular process response to stimulus 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 biological process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus biological regulation negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication tube development respiratory tube development lung development respiratory system development primary metabolic process metabolic process lipid metabolic process pancreas development determination of pancreatic left/right asymmetry transport epithelial cilium movement involved in determination of left/right asymmetry establishment of localization localization epithelial cilium movement involved in extracellular fluid movement extracellular transport microtubule-based transport microtubule-based movement microtubule-based process cilium movement ureter development renal system development regulation of developmental process cellular developmental process negative regulation of developmental process regulation of cell differentiation cell differentiation negative regulation of cell differentiation maintenance of animal organ identity 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 non-motile cilium assembly tissue morphogenesis anatomical structure morphogenesis epithelium development convergent extension morphogenesis of an epithelium tissue development multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis retina homeostasis photoreceptor cell maintenance heart development cardiac atrium development circulatory system development cardiac septum development cardiac chamber development atrial septum development regulation of Wnt signaling pathway, planar cell polarity pathway Wnt signaling pathway, planar cell polarity pathway regulation of non-canonical Wnt signaling pathway non-canonical Wnt signaling pathway establishment or maintenance of cell polarity convergent extension involved in gastrulation embryonic morphogenesis embryo development gastrulation digestive system development digestive tract development determination of intestine left/right asymmetry determination of digestive tract left/right asymmetry kidney morphogenesis animal organ morphogenesis kidney development determination of stomach left/right asymmetry stomach development heart morphogenesis embryonic heart tube development tube morphogenesis embryonic heart tube morphogenesis heart looping epithelial tube morphogenesis embryonic organ development embryonic organ morphogenesis determination of heart left/right asymmetry	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection ciliary inversin compartment intracellular anatomical structure cytoplasm cytosol extracellular region ciliary base
A, C [auth G]	Protein unc-119 homolog A	binding lipid binding	localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization lipoprotein transport intracellular protein localization lipoprotein localization establishment of localization mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cellular process localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization lipoprotein transport intracellular protein localization lipoprotein localization establishment of localization mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cellular process cytokinesis cell division cell cycle mitotic cell cycle cell cycle process regulation of localization import into cell regulation of cellular process regulation of cellular component organization negative regulation of biological process negative regulation of transport negative regulation of endocytosis caveolin-mediated endocytosis vesicle-mediated transport cellular component organization negative regulation of cellular process cellular component organization or biogenesis regulation of endocytosis regulation of biological process negative regulation of caveolin-mediated endocytosis negative regulation of cellular component organization regulation of transport biological regulation regulation of vesicle-mediated transport regulation of caveolin-mediated endocytosis endocytosis developmental process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development trans-synaptic signaling synaptic signaling signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission cell communication sensory perception of light stimulus system process sensory perception nervous system process visual perception phototransduction cellular response to stimulus detection of light stimulus response to light stimulus detection of external stimulus response to stimulus response to external stimulus detection of abiotic stimulus detection of stimulus response to abiotic stimulus response to radiation signal transduction positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of protein tyrosine kinase activity regulation of kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process peptidyl-tyrosine modification positive regulation of molecular function positive regulation of protein modification process positive regulation of peptidyl-tyrosine phosphorylation protein metabolic process positive regulation of protein kinase activity positive regulation of cellular process positive regulation of protein tyrosine kinase activity regulation of peptidyl-tyrosine phosphorylation positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of phosphorylation peptidyl-tyrosine phosphorylation negative regulation of clathrin-dependent endocytosis clathrin-dependent endocytosis negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis receptor-mediated endocytosis regulation of clathrin-dependent endocytosis	intercellular bridge cellular anatomical structure intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton spindle midzone centrosome microtubule organizing center intercellular bridge cellular anatomical structure intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton spindle midzone centrosome microtubule organizing center synapse cell junction cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
B	IPR019734	Tetratricopeptide repeat	Repeat
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR056883	Nephrocystin 3, helical domain	Domain
B	IPR056885	Nephrocystin-3, TPR-repeats region	Domain
B	IPR056886	Nephrocystin-3, alpha-beta domain	Domain
B	IPR056884	Nephrocystin 3-like, N-terminal	Domain
A, C [auth G]	IPR008015	GMP phosphodiesterase, delta subunit	Domain
A, C [auth G]	IPR051519	PDE6D/unc-119 myristoyl-binding	Family
A, C [auth G]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, C [auth G]	IPR037036	GMP phosphodiesterase, delta subunit superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q7Z494	NPHP3-related Meckel-like syndrome nephronophthisis 3 autosomal recessive polycystic kidney disease nephronophthisis renal-hepatic-pancreatic dysplasia renal-hepatic-pancreatic dysplasia 1 Senior-Loken syndrome Pick disease polydactyly Renal dysplasia and retinal aplasia (disorder) astrocytic tumor congenital anomaly of kidney and urinary tract glioblastoma malignant ependymoma osteosarcoma NPHP3-related Meckel-like syndrome nephronophthisis 3 autosomal recessive polycystic kidney disease nephronophthisis renal-hepatic-pancreatic dysplasia renal-hepatic-pancreatic dysplasia 1 Senior-Loken syndrome Pick disease polydactyly Renal dysplasia and retinal aplasia (disorder) astrocytic tumor congenital anomaly of kidney and urinary tract glioblastoma malignant ependymoma osteosarcoma pilocytic astrocytoma primitive neuroectodermal tumor Sjogren syndrome atypical teratoid rhabdoid tumor breast carcinoma intellectual disability malignant glioma ovarian cancer polycystic kidney disease 4 progressive supranuclear palsy autosomal dominant polycystic kidney disease cholestasis ciliopathy invasive ductal breast carcinoma myopathy
A, C [auth G]	Pharos: Q13432	cone-rod dystrophy retinitis pigmentosa idiopathic CD4 lymphocytopenia idiopathic CD4-positive T-lymphocytopenia medulloblastoma psoriasis retinal degeneration

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.