3UYS | pdb_00003uys

Crystal structure of apo human ck1d

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3uysd_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3uysc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3uysb_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3uysa_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8080849	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8080849	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8080849	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8080849	3000066	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)
D	Pkinase	e3uysD2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Pkinase	ECOD (develop294)
C	RRM_1	e3uysC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
B	PK_Tyr_Ser-Thr	e3uysB2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: PK_Tyr_Ser-Thr	ECOD (develop294)
A	AIG1	e3uysA1	A: alpha bundles	X: ETN0001 domain-like	H: ETN0001 domain-like	T: NAC/WRKY/GCM/WOPR domain	F: AIG1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Casein kinase I isoform delta	protein serine/threonine kinase activity tau-protein kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding protein serine/threonine kinase activity tau-protein kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cell adhesion molecule binding cadherin binding protein binding	localization protein localization to cilium protein localization to organelle macromolecule localization intracellular protein localization protein localization to microtubule cytoskeleton protein localization to cytoskeleton protein localization to microtubule organizing center protein localization to centrosome rhythmic process regulation of biological process circadian rhythm biological regulation regulation of circadian rhythm localization protein localization to cilium protein localization to organelle macromolecule localization intracellular protein localization protein localization to microtubule cytoskeleton protein localization to cytoskeleton protein localization to microtubule organizing center protein localization to centrosome rhythmic process regulation of biological process circadian rhythm biological regulation regulation of circadian rhythm cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of non-canonical Wnt signaling pathway positive regulation of Wnt signaling pathway non-canonical Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of signaling regulation of Wnt signaling pathway cell surface receptor signaling pathway regulation of non-canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling import into cell transport endocytosis establishment of localization vesicle-mediated transport establishment of organelle localization vesicle budding from membrane cellular localization vesicle targeting, to, from or within Golgi vesicle targeting cellular component organization vesicle organization cellular component biogenesis cellular component assembly organelle localization establishment of localization in cell protein-containing complex assembly vesicle coating cellular component organization or biogenesis vesicle targeting, rough ER to cis-Golgi membrane organization vesicle localization protein-containing complex organization establishment of vesicle localization intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport organelle organization COPII-coated vesicle budding COPII vesicle coating Golgi vesicle transport positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process regulation of biosynthetic process circadian regulation of gene expression gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process organelle assembly microtubule cytoskeleton organization membraneless organelle assembly spindle assembly microtubule-based process cell cycle cytoskeleton organization chromosome segregation spindle organization cell cycle process plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cilium assembly non-motile cilium assembly cilium organization cell projection assembly protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process protein localization to Golgi apparatus developmental process multicellular organismal process head development dopaminergic neuron differentiation cellular developmental process animal organ development brain development nervous system development generation of neurons multicellular organism development neurogenesis central nervous system neuron differentiation central nervous system development neuron differentiation cell differentiation midbrain development anatomical structure development midbrain dopaminergic neuron differentiation system development regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of canonical Wnt signaling pathway Golgi organization endomembrane system organization protein polymerization microtubule polymerization microtubule polymerization or depolymerization microtubule nucleation supramolecular fiber organization	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection sperm end piece 9+2 motile cilium sperm flagellum motile cilium intracellular organelle intracellular anatomical structure cytoskeleton membraneless organelle membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection sperm end piece 9+2 motile cilium sperm flagellum motile cilium intracellular organelle intracellular anatomical structure cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton centrosome microtubule organizing center microtubule cytoskeleton cytoplasm cytosol cell periphery plasma membrane membrane sperm principal piece nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen Golgi apparatus endomembrane system bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle membrane perinuclear region of cytoplasm spindle polymeric cytoskeletal fiber spindle microtubule supramolecular fiber microtubule supramolecular polymer supramolecular complex ciliary basal body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR050235	Casein kinase 1/Serine/threonine-protein kinase-like	Family
A, B, C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P48730	advanced sleep phase syndrome 2 Advanced Sleep-Phase Syndrome, Familial renal cell carcinoma atypical teratoid rhabdoid tumor cutaneous lupus erythematosus invasive ductal breast carcinoma major depressive disorder malignant mesothelioma osteosarcoma plasma cell myeloma schizophrenia bipolar disorder gastrointestinal stromal tumor Kleine-Levin syndrome malignant ependymoma advanced sleep phase syndrome 2 Advanced Sleep-Phase Syndrome, Familial renal cell carcinoma atypical teratoid rhabdoid tumor cutaneous lupus erythematosus invasive ductal breast carcinoma major depressive disorder malignant mesothelioma osteosarcoma plasma cell myeloma schizophrenia bipolar disorder gastrointestinal stromal tumor Kleine-Levin syndrome malignant ependymoma ovarian cancer psoriasis tuberculosis astrocytic tumor breast carcinoma glioblastoma lung cancer malignant glioma oligodendroglioma

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.