2V5Q | pdb_00002v5q

CRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WITH A SELECTIVE DARPIN

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)
C	d2v5qc1	Designed proteins	Artificial ankyrin repeat proteins	Artificial ankyrin repeat proteins	Artificial ankyrin repeat proteins	4ank	(synthetic construct ) [TaxId: 32630 ],	SCOPe (2.08)
C	d2v5qc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(synthetic construct ) [TaxId: 32630 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062400	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062400	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	Tailspike_C	e2v5qD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Tailspike_C	ECOD (develop294)
C	E3_binding	e2v5qC1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: E3_binding	ECOD (develop294)
B	Tailspike_C	e2v5qB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Tailspike_C	ECOD (develop294)
A	Tailspike_C	e2v5qA1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Tailspike_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
C	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	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	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
C, D	DESIGN ANKYRIN REPEAT PROTEIN	-	-	-
A, B	SERINE/THREONINE-PROTEIN KINASE PLK1	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 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 cytoskeletal protein binding microtubule binding protein binding tubulin binding 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 identical protein binding protein serine kinase activity cation binding magnesium ion binding metal ion binding protein-containing complex binding anaphase-promoting complex binding kinase binding enzyme binding protein kinase binding protein serine/threonine kinase activity	cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination DNA damage response regulation of response to stimulus metabolic process cellular process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of chromosome segregation regulation of cell cycle phase transition regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation cell cycle process regulation of cell cycle process chromosome organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition organelle organization mitotic cell cycle process regulation of sister chromatid segregation nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition regulation of cytoskeleton organization microtubule cytoskeleton organization regulation of mitotic spindle organization membraneless organelle assembly cellular component biogenesis cellular component assembly regulation of mitotic spindle assembly mitotic sister chromatid segregation microtubule cytoskeleton organization involved in mitosis spindle organization mitotic nuclear division organelle assembly organelle fission regulation of microtubule-based process regulation of spindle organization regulation of cellular component biogenesis spindle assembly mitotic spindle organization regulation of spindle assembly mitotic spindle assembly nuclear division regulation of organelle assembly microtubule-based process cytoskeleton organization regulation of microtubule cytoskeleton organization mitotic chromosome condensation chromosome condensation membrane organization cellular component disassembly nuclear membrane disassembly membrane disassembly nuclear membrane organization mitotic nuclear membrane disassembly nucleus organization nuclear envelope organization endomembrane system organization sister chromatid cohesion positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic 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 positive regulation of cellular process regulation of protein metabolic process proteasomal protein catabolic 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 ubiquitin-dependent protein catabolic process regulation of protein catabolic process regulation of cytokinesis cytokinesis regulation of cell division cell division protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process double-strand break repair via nonhomologous end joining double-strand break repair via alternative nonhomologous end joining RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cell cycle G2/M phase transition G2/M transition of mitotic cell cycle regulation of localization protein localization to cell periphery regulation of protein localization regulation of protein localization to cell periphery localization regulation of protein localization to cell cortex macromolecule localization intracellular protein localization protein localization to cell cortex meiotic chromosome segregation sexual reproduction reproductive process meiotic cell cycle multicellular organismal reproductive process female gamete generation meiotic cell cycle process gamete generation female meiotic nuclear division meiotic nuclear division female meiosis chromosome segregation positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus protein localization to organelle positive regulation of protein localization microtubule bundle formation cytoskeleton-dependent cytokinesis mitotic cytokinesis establishment of protein localization establishment of localization positive regulation of organelle organization regulation of mitotic nuclear division positive regulation of mitotic nuclear division positive regulation of mitotic metaphase/anaphase transition positive regulation of mitotic cell cycle phase transition mitotic sister chromatid separation positive regulation of nuclear division regulation of chromosome separation regulation of mitotic sister chromatid separation positive regulation of cellular component organization positive regulation of metaphase/anaphase transition of cell cycle positive regulation of cell cycle process positive regulation of mitotic cell cycle positive regulation of cell cycle chromosome separation positive regulation of cell cycle phase transition positive regulation of mitotic sister chromatid separation regulation of nuclear division positive regulation of chromosome separation negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death protein localization to chromatin protein localization to chromosome spindle checkpoint signaling negative regulation of cell cycle intracellular signal transduction negative regulation of mitotic cell cycle cell communication negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling signal transduction negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling negative regulation of cellular component organization regulation of mitotic sister chromatid segregation negative regulation of mitotic nuclear division signaling spindle assembly checkpoint signaling negative regulation of mitotic metaphase/anaphase transition negative regulation of chromosome separation negative regulation of mitotic cell cycle phase transition negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling negative regulation of chromosome segregation negative regulation of nuclear division negative regulation of organelle organization negative regulation of mitotic sister chromatid separation negative regulation of metaphase/anaphase transition of cell cycle mitotic cytokinetic process cleavage furrow formation cytokinetic process membrane invagination plasma membrane invagination mitotic cleavage furrow formation positive regulation of mitotic nuclear envelope disassembly regulation of mitotic nuclear envelope disassembly regulation of membrane disassembly astral microtubule organization cytoplasmic microtubule organization supramolecular fiber organization DNA damage checkpoint signaling mitotic G2 DNA damage checkpoint signaling mitotic G2/M transition checkpoint mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling regulation of G2/M transition of mitotic cell cycle DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle G2/M phase transition signal transduction in response to DNA damage negative regulation of G2/M transition of mitotic cell cycle synaptonemal complex disassembly synaptonemal complex organization Golgi inheritance organelle inheritance Golgi organization microtubule organizing center organization centrosome cycle meiosis I meiosis I cell cycle process homologous chromosome segregation regulation of anaphase-promoting complex-dependent catabolic process anaphase-promoting complex-dependent catabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton spindle midzone cytoplasm cytosol protein-containing complex intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton spindle midzone cytoplasm cytosol protein-containing complex chromosome chromosomal region kinetochore chromosome, centromeric region outer kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome chromatin mitotic spindle mitotic spindle pole midbody centrosome microtubule organizing center centriolar satellite centriole membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen condensed nuclear chromosome nuclear chromosome synaptonemal structure synaptonemal complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR000959	POLO box domain	Domain
A, B	IPR033695	Second polo-box domain	Domain
A, B	IPR033702	Polo-like kinase 1, catalytic domain	Domain
A, B	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B	IPR036947	POLO box domain superfamily	Homologous Superfamily
A, B	IPR033701	First polo-box domain	Domain
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P53350	malignant glioma leukemia mixed glioma atypical teratoid rhabdoid tumor cancer hepatocellular carcinoma malignant mesothelioma non-small cell lung carcinoma squamous cell lung carcinoma breast cancer glioblastoma invasive ductal breast carcinoma lung adenocarcinoma medulloblastoma osteosarcoma malignant glioma leukemia mixed glioma atypical teratoid rhabdoid tumor cancer hepatocellular carcinoma malignant mesothelioma non-small cell lung carcinoma squamous cell lung carcinoma breast cancer glioblastoma invasive ductal breast carcinoma lung adenocarcinoma medulloblastoma osteosarcoma breast carcinoma glioma large cell medulloblastoma psoriasis

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.