1FQ1

CRYSTAL STRUCTURE OF KINASE ASSOCIATED PHOSPHATASE (KAP) IN COMPLEX WITH PHOSPHO-CDK2

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	d1fq1a_	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Dual specificity phosphatase-like	Kinase associated phosphatase (kap)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1fq1b_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Cyclin-dependent PK, CDK2	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	(Phosphotyrosine protein) phosphatases II	8033188	3000304	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8040310	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	PF05706	e1fq1A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: PF05706	ECOD (1.6)
B	PF00069	e1fq1B1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PF00069	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	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	PF05706	Cyclin-dependent kinase inhibitor 3 (CDKN3) (CDKN3)	Cyclin-dependent kinase inhibitor 3 (CDKN3)	This family consists of cyclin-dependent kinase inhibitor 3 or kinase associated phosphatase proteins from several mammalian species. The cyclin-dependent kinase (Cdk)-associated protein phosphatase (KAP) is a human dual specificity protein phosphata ...	This family consists of cyclin-dependent kinase inhibitor 3 or kinase associated phosphatase proteins from several mammalian species. The cyclin-dependent kinase (Cdk)-associated protein phosphatase (KAP) is a human dual specificity protein phosphatase that dephosphorylates Cdk2 on threonine 160 in a cyclin-dependent manner [1,2].	Domain
B	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	CYCLIN-DEPENDENT KINASE INHIBITOR 3	phosphoric ester hydrolase activity phosphoprotein phosphatase activity protein serine/threonine phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds myosin phosphatase activity phosphatase activity hydrolase activity catalytic activity protein tyrosine/serine/threonine phosphatase activity protein tyrosine phosphatase activity	negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process regulation of cell cycle regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of cyclin-dependent protein kinase activity regulation of transferase activity regulation of primary metabolic process organic substance metabolic process regulation of cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorylation regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process dephosphorylation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol perinuclear region of cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B	CELL DIVISION PROTEIN KINASE 2	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity cyclin-dependent protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein binding protein domain specific binding cyclin binding protein serine kinase activity cation binding magnesium ion binding metal ion binding	response to organic substance response to stimulus response to chemical cellular process cell division microtubule organizing center organization microtubule cytoskeleton organization cellular component organization centrosome duplication organelle organization centrosome cycle microtubule-based process cell cycle cellular component organization or biogenesis response to organic substance response to stimulus response to chemical cellular process cell division microtubule organizing center organization microtubule cytoskeleton organization cellular component organization centrosome duplication organelle organization centrosome cycle microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization cell cycle process regulation of biosynthetic process regulation of biological process regulation of cellular process cellular biosynthetic process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organic substance metabolic process biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process organic cyclic compound metabolic process DNA replication positive regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic cyclic compound biosynthetic process cellular response to stimulus regulation of cell cycle phase transition DNA damage checkpoint signaling signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction regulation of cell cycle negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle DNA damage response signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition cellular senescence centriole assembly organelle assembly non-membrane-bounded organelle assembly cellular component biogenesis cellular component assembly centriole replication organonitrogen compound metabolic process macromolecule modification protein metabolic process post-translational protein modification protein modification process protein phosphorylation phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process DNA repair cell cycle G2/M phase transition regulation of G2/M transition of mitotic cell cycle G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process cellular response to nitrogen compound cellular response to inorganic substance response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to inorganic substance cellular response to nitric oxide cellular response to chemical stimulus response to nitric oxide cellular response to reactive nitrogen species regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation regulation of DNA-templated DNA replication positive regulation of DNA-templated DNA replication positive regulation of DNA-templated DNA replication initiation small GTPase-mediated signal transduction Ras protein signal transduction intracellular signaling cassette localization transport monoatomic ion transport potassium ion transport monoatomic cation transport establishment of localization metal ion transport cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of cellular process positive regulation of macromolecule biosynthetic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process catabolic process regulation of anaphase-promoting complex-dependent catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis organonitrogen compound catabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of protein catabolic process sexual reproduction reproductive process meiotic cell cycle positive regulation of organelle organization chromatin organization regulation of heterochromatin formation regulation of chromatin organization regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization negative regulation of gene expression negative regulation of gene expression, epigenetic regulation of cellular component organization positive regulation of cellular component organization protein-DNA complex organization positive regulation of heterochromatin formation positive regulation of chromatin organization chromatin remodeling heterochromatin formation protein-containing complex organization positive regulation of cellular component biogenesis epigenetic regulation of gene expression chromosome organization regulation of cellular component biogenesis	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol transcription regulator complex sex chromosome intracellular non-membrane-bounded organelle chromosome non-membrane-bounded organelle X chromosome Cajal body membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen Y chromosome cyclin E2-CDK2 complex male germ cell nucleus germ cell nucleus chromosome, telomeric region chromosomal region cyclin A2-CDK2 complex condensed chromosome centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cyclin E1-CDK2 complex endosome intracellular vesicle cytoplasmic vesicle vesicle cyclin A1-CDK2 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A	IPR020422	Dual specificity protein phosphatase domain	Domain
A	IPR022778	CDKN3 domain	Domain
A	IPR008425	Cyclin-dependent kinase inhibitor 3	Family
B	IPR000719	Protein kinase domain	Domain
B	IPR017441	Protein kinase, ATP binding site	Binding Site
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q16667	Liver Cirrhosis, Experimental hepatocellular carcinoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm acute myeloid leukemia ulcerative colitis atopic eczema breast carcinoma endometriosis interstitial cystitis liver cancer lung adenocarcinoma malignant glioma Liver Cirrhosis, Experimental hepatocellular carcinoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm acute myeloid leukemia ulcerative colitis atopic eczema breast carcinoma endometriosis interstitial cystitis liver cancer lung adenocarcinoma malignant glioma medulloblastoma ovarian cancer primitive neuroectodermal tumor adrenal cortex carcinoma atypical teratoid rhabdoid tumor cancer glioblastoma invasive ductal breast carcinoma lung cancer malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma psoriasis astrocytic tumor breast cancer ductal breast carcinoma in situ hepatoblastoma IgA glomerulonephritis large cell medulloblastoma
B	Pharos: P24941	melanoma glioblastoma large cell medulloblastoma malignant glioma medulloblastoma osteosarcoma primitive neuroectodermal tumor adrenal cortex carcinoma vitiligo alopecia areata atypical teratoid rhabdoid tumor Childhood Diffuse Large B-Cell Lymphoma diffuse large B-cell lymphoma malignant colon neoplasm pilocytic astrocytoma melanoma glioblastoma large cell medulloblastoma malignant glioma medulloblastoma osteosarcoma primitive neuroectodermal tumor adrenal cortex carcinoma vitiligo alopecia areata atypical teratoid rhabdoid tumor Childhood Diffuse Large B-Cell Lymphoma diffuse large B-cell lymphoma malignant colon neoplasm pilocytic astrocytoma psoriasis asthma breast disease cleft lip eye disease Hashimoto thyroiditis hypothyroidism malignant ependymoma malignant mesothelioma polycystic ovary syndrome rheumatoid arthritis allergic rhinitis attention deficit hyperactivity disorder, inattentive type cancer cutaneous melanoma gastroesophageal reflux disease hematologic disease

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.