8PYR | pdb_00008pyr

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

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family 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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Amino_oxidase	e8pyrD01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: Amino_oxidase	ECOD (v294.1)

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 (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, F	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
B, F	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
C, G	PF25811	MAT1 C-terminal CAK anchor (CAK-anch_MAT1)	MAT1 C-terminal CAK anchor	-	Disordered

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 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 kinase activity RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat S5 kinase activity	regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular process cell division 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 regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular process cell division 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 nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair regulation of biological process regulation of cellular process cell cycle regulation of cell cycle snRNA transcription snRNA metabolic process snRNA transcription by RNA polymerase II 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 DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process 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 transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	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 cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane 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 cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane RNA polymerase II transcription regulator complex membrane-bounded organelle 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 intracellular organelle lumen nucleoplasm transcription factor TFIIH holo complex transcription factor TFIIK complex nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex RNA polymerase complex nuclear cyclin-dependent protein kinase holoenzyme complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen CAK-ERCC2 complex perinuclear region of cytoplasm intracellular membraneless organelle nucleolus fibrillar center membraneless organelle male germ cell nucleus germ cell nucleus
B, F	Cyclin-H	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity cyclin-dependent protein kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	regulation of protein stability biological regulation regulation of biological quality protein stabilization RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of protein stability biological regulation regulation of biological quality protein stabilization RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process transcription initiation at RNA polymerase II promoter 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 macromolecule metabolic 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 cell cycle regulation of cell cycle G1/S transition of mitotic cell cycle cell cycle process mitotic cell cycle phase transition	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 RNA polymerase II transcription regulator complex membrane-bounded organelle intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex 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 RNA polymerase II transcription regulator complex membrane-bounded organelle intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm transcription factor TFIIH holo complex transcription factor TFIIK complex nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex RNA polymerase complex nuclear cyclin-dependent protein kinase holoenzyme complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen male germ cell nucleus germ cell nucleus 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 cyclin-dependent protein kinase regulator 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 cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity cyclin-dependent protein kinase regulator 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	response to stimulus response to metal ion response to chemical response to calcium ion regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process response to stimulus response to metal ion response to chemical response to calcium ion regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process transcription initiation at RNA polymerase II promoter 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 macromolecule metabolic 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	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 RNA polymerase II transcription regulator complex membrane-bounded organelle intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex 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 RNA polymerase II transcription regulator complex membrane-bounded organelle intracellular anatomical structure transcription factor TFIIH core complex nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm transcription factor TFIIH holo complex transcription factor TFIIK complex nuclear DNA-directed RNA polymerase complex organelle lumen carboxy-terminal domain protein kinase complex RNA polymerase complex nuclear cyclin-dependent protein kinase holoenzyme complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen CAK-ERCC2 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	IPR050108	Cyclin-dependent kinase	Family
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	IPR057657	MAT1, C-terminal CAK anchor	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	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.