4YU2 | pdb_00004yu2

Crystal structure of DYRK1A with harmine-derivatized AnnH-75 inhibitor

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4yu2a_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4yu2d_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4yu2c_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4yu2b_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	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)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8079155	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8079155	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8079155	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8079155	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)
A	GFP	e4yu2A1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: GFP	ECOD (v294.1)
D	SBP_bac_5	e4yu2D1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: SBP_bac_5	ECOD (v294.1)
C	SBP_bac_5	e4yu2C1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: SBP_bac_5	ECOD (v294.1)
B	SBP_bac_5	e4yu2B1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: SBP_bac_5	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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	Dual specificity tyrosine-phosphorylation-regulated kinase 1A	protein serine/threonine/tyrosine 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 cytoskeletal protein binding protein binding binding tubulin binding transcription coactivator activity transcription regulator activity protein serine/threonine/tyrosine 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 cytoskeletal protein binding protein binding binding tubulin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein serine/threonine kinase activity histone H3T45 kinase activity histone H3 kinase activity histone modifying activity histone kinase activity tau-protein kinase activity protein serine kinase activity protein tyrosine kinase activity 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 non-membrane spanning protein tyrosine kinase activity tau protein binding actin binding splicing factor binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity identical protein binding	regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of biological process negative regulation of metabolic process regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of biological process negative regulation of metabolic process primary metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of mRNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of mRNA processing RNA splicing biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process negative regulation of RNA splicing RNA splicing, via transesterification reactions negative regulation of biosynthetic process mRNA splicing, via spliceosome cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process rhythmic process circadian rhythm regulation of cellular component organization negative regulation of heterochromatin formation positive regulation of biological process negative regulation of chromatin organization positive regulation of macromolecule biosynthetic process cellular component organization cellular component biogenesis positive regulation of metabolic process cellular component assembly positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process regulation of heterochromatin formation heterochromatin formation regulation of chromatin organization negative regulation of cellular component organization epigenetic regulation of gene expression heterochromatin organization positive regulation of gene expression regulation of heterochromatin organization negative regulation of gene expression, epigenetic negative regulation of heterochromatin organization amyloid precursor protein catabolic process regulation of amyloid-beta formation regulation of protein metabolic process regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process protein metabolic process amyloid precursor protein metabolic process amyloid-beta formation regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization microtubule cytoskeleton organization regulation of protein-containing complex assembly microtubule polymerization or depolymerization protein-containing complex assembly negative regulation of protein polymerization negative regulation of supramolecular fiber organization protein polymerization negative regulation of microtubule polymerization or depolymerization protein-containing complex organization negative regulation of cytoskeleton organization regulation of microtubule-based process negative regulation of microtubule polymerization microtubule polymerization regulation of cellular component biogenesis regulation of organelle organization negative regulation of protein-containing complex assembly organelle organization negative regulation of organelle organization regulation of protein polymerization regulation of microtubule polymerization regulation of supramolecular fiber organization microtubule-based process supramolecular fiber organization cytoskeleton organization regulation of microtubule cytoskeleton organization alternative mRNA splicing, via spliceosome regulation of alternative mRNA splicing, via spliceosome cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction negative regulation of cell communication cell communication cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator negative regulation of DNA damage response, signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus signal transduction by p53 class mediator negative regulation of signal transduction regulation of response to stimulus DNA damage response regulation of cell communication signal transduction in response to DNA damage regulation of inclusion body assembly inclusion body assembly neurofibrillary tangle assembly regulation of neurofibrillary tangle assembly protein phosphorylation protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process positive regulation of RNA splicing peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation developmental process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development positive regulation of DNA-templated transcription DNA-templated transcription regulation of RNA biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection axon protein-containing complex ribonucleoprotein complex

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	IPR050494	Serine/threonine and dual-specificity kinase	Family
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR044131	Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
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: Q13627	DYRK1A-related intellectual disability syndrome intellectual disability Neurodevelopmental Disorders Down syndrome acute myeloid leukemia cerebrovascular disorder microcephaly ovarian cancer attention deficit hyperactivity disorder, inattentive type dermatomyositis epilepsy juvenile dermatomyositis pancreatic intraductal papillary-mucinous neoplasm autism spectrum disorder lymphoplasmacytic lymphoma DYRK1A-related intellectual disability syndrome intellectual disability Neurodevelopmental Disorders Down syndrome acute myeloid leukemia cerebrovascular disorder microcephaly ovarian cancer attention deficit hyperactivity disorder, inattentive type dermatomyositis epilepsy juvenile dermatomyositis pancreatic intraductal papillary-mucinous neoplasm autism spectrum disorder lymphoplasmacytic lymphoma osteosarcoma plasma cell myeloma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048

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.