8PYR

Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

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)	8042855	3000066	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Protein kinase-like (PK-like)	8042855	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8037906	3000768	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8037909	3000768	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cyclin-like	8037909	3000768	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cyclin-like	8037906	3000768	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D, H	Heavy Chain	IGHV3	-	cyclin-dependent kinase 7	SAbDab (2024-05-03)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	Cyclin-dependent kinase 7	ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 cyclin-dependent protein kinase activity RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular process 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 regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular process 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 cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process regulation of biological process regulation of cellular process regulation of cell cycle snRNA metabolic process snRNA transcription by RNA polymerase II snRNA transcription 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 regulation of cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process protein metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation regulation of protein metabolic process regulation of cellular 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 regulation of metabolic process regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle mitotic cell cycle process G1/S transition of mitotic cell cycle cell cycle process mitotic cell cycle phase transition positive regulation of macromolecule biosynthetic 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 positive regulation of nucleobase-containing compound 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 positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle organelle RNA polymerase II, holoenzyme membrane-enclosed lumen 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 CAK-ERCC2 complex perinuclear region of cytoplasm nucleolus fibrillar center intracellular non-membrane-bounded organelle non-membrane-bounded organelle cyclin-dependent protein kinase holoenzyme complex cyclin-dependent protein kinase activating kinase holoenzyme complex enzyme activator complex nuclear cyclin-dependent protein kinase holoenzyme complex male germ cell nucleus germ cell nucleus
B, F	Cyclin-H	enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	cellular process cell cycle regulation of protein stability biological regulation regulation of biological quality protein stabilization 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 cellular process cell cycle regulation of protein stability biological regulation regulation of biological quality protein stabilization 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 macromolecule metabolic process 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 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 regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle mitotic cell cycle process regulation of cell cycle G1/S transition of mitotic cell cycle cell cycle process mitotic cell cycle phase transition	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle RNA polymerase II, holoenzyme membrane-enclosed lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle RNA polymerase II, holoenzyme membrane-enclosed lumen 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 cyclin-dependent protein kinase holoenzyme complex cyclin-dependent protein kinase activating kinase holoenzyme complex enzyme activator complex nuclear cyclin-dependent protein kinase holoenzyme complex CAK-ERCC2 complex
C, G	CDK-activating kinase assembly factor MAT1	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 transition metal ion binding zinc ion 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 transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis negative regulation of ATP-dependent activity regulation of ATP-dependent activity regulation of cellular component organization regulation of cellular process regulation of catalytic activity negative regulation of biological process DNA geometric change cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis negative regulation of ATP-dependent activity regulation of ATP-dependent activity regulation of cellular component organization regulation of cellular process regulation of catalytic activity negative regulation of biological process DNA geometric change negative regulation of catalytic activity DNA conformation change negative regulation of chromosome organization negative regulation of DNA duplex unwinding negative regulation of cellular process negative regulation of helicase activity negative regulation of DNA helicase activity DNA duplex unwinding regulation of biological process negative regulation of cellular component organization biological regulation negative regulation of molecular function chromosome organization regulation of chromosome organization regulation of DNA duplex unwinding regulation of organelle organization regulation of helicase activity regulation of molecular function organelle organization regulation of DNA helicase activity negative regulation of organelle organization response to stimulus response to metal ion response to chemical response to calcium ion response to inorganic substance 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 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 cellular response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair 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 cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation positive regulation of biological process smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation positive regulation of cellular process nucleotide-excision 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 developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development adult heart development circulatory system development system development regulation of cell cycle phase transition regulation of cell cycle process regulation of cell cycle G1/S phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle regulation of cell cycle head development brain development nervous system development central nervous system development ventricular system development	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle RNA polymerase II, holoenzyme membrane-enclosed lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle RNA polymerase II, holoenzyme membrane-enclosed lumen 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 CAK-ERCC2 complex cyclin-dependent protein kinase holoenzyme complex cyclin-dependent protein kinase activating kinase holoenzyme complex enzyme activator complex nuclear cyclin-dependent protein kinase holoenzyme complex
D, H	Nanobody (VHH-RD7-04)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR017441	Protein kinase, ATP binding site	Binding Site
A, E	IPR000719	Protein kinase domain	Domain
A, E	IPR037770	Cyclin-dependent kinase 7	Family
A, E	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, E	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B, F	IPR031658	Cyclin, C-terminal domain 2	Domain
B, F	IPR006671	Cyclin, N-terminal	Domain
B, F	IPR027081	CyclinH/Ccl1	Family
B, F	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B, F	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
B, F	IPR013763	Cyclin-like domain	Domain
C, G	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
C, G	IPR004575	Cdk-activating kinase assembly factor MAT1/Tfb3	Family
C, G	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C, G	IPR015877	Cdk-activating kinase assembly factor MAT1, centre	Domain
C, G	IPR003903	Ubiquitin interacting motif	Conserved Site
C, G	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, E	Pharos: P50613	peripheral nervous system disease peripheral neuropathy
B, F	Pharos: P51946	sarcomatoid carcinoma carcinoma Mammary Neoplasms, Experimental osteosarcoma prostate carcinoma undifferentiated carcinoma diabetes mellitus mammary neoplasms, animal ovarian cancer lung cancer Pick disease tuberculosis
C, G	Pharos: P51948	lung cancer prostate carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, E	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
A, E	TPO	Parent Component: THR RESID: AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , 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.