5EFQ

Crystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride

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	d5efqa_	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	d5efqc_	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	d5efqb1	All alpha proteins	Cyclin-like	Cyclin-like	Cyclin	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5efqd1	All alpha proteins	Cyclin-like	Cyclin-like	Cyclin	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	SCOP2 Family	Protein kinases catalytic domain-like	8062586	4003661	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Protein kinase-like (PK-like)	8062587	3000066	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062587	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8034372	3000768	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8034370	3000768	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cyclin-like	8034370	3000768	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cyclin-like	8034372	3000768	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	Pkinase_Tyr	e5efqA1	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: Pkinase_Tyr	ECOD (1.6)
C	Pkinase_Tyr	e5efqC1	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: Pkinase_Tyr	ECOD (1.6)
B	Cyclin_N_1	e5efqB2	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_N_1	ECOD (1.6)
D	Cyclin_N_1	e5efqD1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_N_1	ECOD (1.6)

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)
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	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
D	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain
B, D	PF00134	Cyclin, N-terminal domain (Cyclin_N)	Cyclin, N-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.	Domain
B, D	PF21797	Cyclin-T2-like, C-terminal domain (CycT2-like_C)	Cyclin-T2-like, C-terminal domain	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P ...	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFB). This domain adopts s cyclin box fold consisting of five helices and a short C-terminal helix [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Cyclin-dependent kinase 13	protein binding binding cyclin binding RNA binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein binding binding cyclin binding RNA binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity cyclin-dependent protein kinase activity kinase binding enzyme binding protein kinase binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	negative regulation of stem cell differentiation developmental process regulation of biological process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of developmental process biological regulation negative regulation of biological process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation negative regulation of cellular process negative regulation of stem cell differentiation developmental process regulation of biological process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of developmental process biological regulation negative regulation of biological process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation negative regulation of cellular process cellular process negative regulation of cell differentiation cellular response to stimulus regulation of signaling response to stimulus signaling regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction hemopoiesis anatomical structure development cell development positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process transcription elongation by RNA polymerase II cellular biosynthetic process positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process alternative mRNA splicing, via spliceosome mRNA processing RNA processing RNA splicing mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex transcription elongation factor complex nuclear protein-containing complex transferase complex protein kinase complex catalytic complex cyclin/CDK positive transcription elongation factor complex cyclin-dependent protein kinase holoenzyme complex transferase complex, transferring phosphorus-containing groups carboxy-terminal domain protein kinase complex serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex cytoplasm cytosol intracellular vesicle ficolin-1-rich granule endomembrane system cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle Golgi apparatus cyclin K-CDK13 complex extracellular region extracellular space
B, D	Cyclin-K	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 binding kinase binding enzyme 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 binding kinase binding enzyme binding protein kinase binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity protein kinase regulator activity kinase activator activity enzyme activator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase activator activity kinase regulator activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process negative regulation by host of viral genome replication biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral life cycle negative regulation by host of viral process modulation by host of viral genome replication biological process involved in symbiotic interaction modulation by host of viral process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process negative regulation by host of viral genome replication biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral life cycle negative regulation by host of viral process modulation by host of viral genome replication biological process involved in symbiotic interaction modulation by host of viral process viral genome replication viral process biological process involved in interaction with symbiont regulation of cellular process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process cell division regulation of signaling signaling regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction transcription by RNA polymerase II regulation of transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II 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 cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process cell cycle phosphorus metabolic process protein modification process regulation of cell cycle protein phosphorylation phosphorylation regulation of protein metabolic process regulation of protein kinase activity 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	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular organelle lumen intracellular organelle nucleoplasm cyclin/CDK positive transcription elongation factor complex intracellular membrane-bounded organelle cellular anatomical entity organelle lumen carboxy-terminal domain protein kinase complex organelle nuclear cyclin-dependent protein kinase holoenzyme complex nuclear lumen cyclin K-CDK13 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR017441	Protein kinase, ATP binding site	Binding Site
A, C	IPR000719	Protein kinase domain	Domain
A, C	IPR050108	Cyclin-dependent kinase	Family
A, C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, C	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B, D	IPR004367	Cyclin, C-terminal domain	Domain
B, D	IPR006671	Cyclin, N-terminal	Domain
B, D	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B, D	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
B, D	IPR013763	Cyclin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: Q14004	congenital heart defects, dysmorphic facial features, and intellectual developmental disorder intellectual disability astrocytic tumor malignant ependymoma microcephaly ovarian cancer juvenile dermatomyositis malignant mesothelioma oligodendroglioma pancreatic ductal adenocarcinoma Gaucher disease Malformations of Cortical Development medulloblastoma osteosarcoma Pick disease
B, D	Pharos: O75909	malignant pancreatic neoplasm pancreatic ductal adenocarcinoma osteosarcoma psoriasis ovarian cancer

Protein Modification Annotation

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

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.