Annotations: 6XI8

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	Protein kinase-like (PK-like)	8103118	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)
B [auth A]	PF00069	e6xi8A1	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)
C [auth B]	PF00134	e6xi8B2	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: PF00134	ECOD (1.6)
C [auth B]	PF16899	e6xi8B1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: PF16899	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C]	PF06391	CDK-activating kinase assembly factor MAT1 (MAT1)	CDK-activating kinase assembly factor MAT1	-	Family
B [auth A]	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain
C [auth B]	PF16899	Cyclin C-terminal domain (Cyclin_C_2)	Cyclin C-terminal domain	Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H [1].	Domain
C [auth B]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	RNA polymerase II transcription factor B subunit 3	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 cation binding ion binding binding 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 cation binding ion binding binding metal ion binding small molecule binding	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair nucleotide-excision repair regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	RNA polymerase II transcription regulator complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm RNA polymerase II transcription regulator complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm transcription factor TFIIH holo complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups transcription factor TFIIK complex nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex organelle RNA polymerase complex serine/threonine protein kinase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
B [auth A]	Serine/threonine-protein kinase KIN28	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 RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress cellular process response to starvation cell division cellular biosynthetic process cellular metabolic process cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress cellular process response to starvation cell division cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process macromolecule metabolic process cell cycle transcription initiation at RNA polymerase II promoter DNA-templated transcription initiation protein phosphorylation organonitrogen compound metabolic process phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process positive regulation of Atg1/ULK1 kinase complex assembly regulation of biological process regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis biological regulation positive regulation of biological process Atg1/ULK1 kinase complex assembly regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of Atg1/ULK1 kinase complex assembly regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process transcription by RNA polymerase I DNA metabolic process nucleotide-excision repair DNA damage response DNA repair positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process 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 regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process 7-methylguanosine RNA capping RNA capping mRNA processing RNA processing 7-methylguanosine mRNA capping mRNA metabolic process RNA 5'-end processing positive regulation of autophagy catabolic process autophagy regulation of catabolic process regulation of autophagy cellular catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process process utilizing autophagic mechanism	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol RNA polymerase II transcription regulator complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol RNA polymerase II transcription regulator complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm transcription factor TFIIH holo complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups transcription factor TFIIK complex nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex organelle RNA polymerase complex serine/threonine protein kinase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
C [auth B]	Cyclin CCL1	enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation positive regulation of Atg1/ULK1 kinase complex assembly regulation of biological process regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis biological regulation positive regulation of biological process Atg1/ULK1 kinase complex assembly regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of Atg1/ULK1 kinase complex assembly regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process DNA metabolic process nucleotide-excision repair DNA damage response DNA repair regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of autophagy catabolic process autophagy positive regulation of cellular metabolic process regulation of catabolic process regulation of autophagy cellular catabolic process positive regulation of catabolic process positive regulation of metabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process process utilizing autophagic mechanism	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle RNA polymerase II transcription regulator complex RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle RNA polymerase II transcription regulator complex RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen protein kinase complex nucleoplasm transcription factor TFIIH holo complex catalytic complex transferase complex, transferring phosphorus-containing groups transcription factor TFIIK complex nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex RNA polymerase complex serine/threonine protein kinase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A [auth C]	IPR004575	Cdk-activating kinase assembly factor MAT1/Tfb3	Family
A [auth C]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth C]	IPR015877	Cdk-activating kinase assembly factor MAT1, centre	Domain
A [auth C]	IPR001841	Zinc finger, RING-type	Domain
B [auth A]	IPR017441	Protein kinase, ATP binding site	Binding Site
B [auth A]	IPR000719	Protein kinase domain	Domain
B [auth A]	IPR037770	Cyclin-dependent kinase 7	Family
B [auth A]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B [auth A]	IPR008271	Serine/threonine-protein kinase, active site	Active Site
C [auth B]	IPR031658	Cyclin, C-terminal domain 2	Domain
C [auth B]	IPR006671	Cyclin, N-terminal	Domain
C [auth B]	IPR027081	CyclinH/Ccl1	Family
C [auth B]	IPR036915	Cyclin-like superfamily	Homologous Superfamily
C [auth B]	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
C [auth B]	IPR013763	Cyclin-like domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth A]	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 R01GM133198.