2PMI | pdb_00002pmi

Structure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-responsive Signal Transduction Pathway with Bound ATP-gamma-S

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2pmia_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2pmic_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

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)	8062583	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062583	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)
A	Abhydrolase_1	e2pmiA1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
C	Abhydrolase_1	e2pmiC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
B	Abhydrolase_1	e2pmiB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
D	Abhydrolase_1	e2pmiD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)

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	PF08613	Cyclin (Cyclin)	Cyclin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Cyclin-dependent protein kinase PHO85	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 binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate 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 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	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process regulation of metabolic process lipid metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process regulation of metabolic process lipid metabolic process regulation of primary metabolic process protein destabilization regulation of protein stability regulation of biological quality regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds regulation of glucan biosynthetic process regulation of generation of precursor metabolites and energy regulation of polysaccharide metabolic process polysaccharide metabolic process glucan metabolic process regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process glycogen metabolic process generation of precursor metabolites and energy regulation of macromolecule metabolic process glycogen biosynthetic process macromolecule biosynthetic process biosynthetic process regulation of polysaccharide biosynthetic process energy reserve metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of carbohydrate biosynthetic process regulation of glycogen metabolic process regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of establishment or maintenance of cell polarity establishment or maintenance of cell polarity fungal-type cell wall organization cellular component organization fungal-type cell wall organization or biogenesis cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization chemical homeostasis homeostatic process lipid homeostasis fatty acid metabolic process long-chain fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process negative regulation of catabolic process catabolic process macroautophagy negative regulation of metabolic process autophagy negative regulation of biological process regulation of catabolic process regulation of autophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy negative regulation of cellular process process utilizing autophagic mechanism regulation of localization cellular localization nucleocytoplasmic transport transport regulation of transport nuclear transport regulation of nucleocytoplasmic transport intracellular transport establishment of localization localization regulation of cellular localization establishment of localization in cell regulation of intracellular transport negative regulation of phosphate metabolic process negative regulation of phosphorus metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process phosphorus metabolic process organelle organization establishment or maintenance of cytoskeleton polarity cytoskeleton organization negative regulation of glycogen biosynthetic process negative regulation of carbohydrate metabolic process negative regulation of glycogen metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process positive regulation of biological process lipid biosynthetic process positive regulation of phosphate metabolic process phospholipid metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of lipid metabolic process positive regulation of cellular process positive regulation of phosphorus metabolic process positive regulation of phospholipid biosynthetic process regulation of phospholipid metabolic process phospholipid biosynthetic process regulation of phospholipid biosynthetic process positive regulation of phospholipid metabolic process positive regulation of lipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process regulation of lipid biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process gene expression nucleic acid metabolic process regulation of gene expression regulation of DNA-templated transcription positive regulation of autophagy positive regulation of catabolic process positive regulation of macroautophagy regulation of protein localization macromolecule localization intracellular protein localization mitotic cell cycle process G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of calcium-mediated signaling negative regulation of signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication cell division regulation of cell division transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA 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 Pho85-Pho80 CDK-cyclin complex cellular bud neck cellular bud site of polarized growth 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 Pho85-Pho80 CDK-cyclin complex cellular bud neck cellular bud site of polarized growth membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B, D	PHO85 cyclin PHO80	protein binding binding kinase binding enzyme binding protein kinase binding 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 localization localization regulation of biological process regulation of protein localization macromolecule localization biological regulation intracellular protein localization cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis regulation of localization localization regulation of biological process regulation of protein localization macromolecule localization biological regulation intracellular protein localization cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process regulation of calcium-mediated signaling signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of calcium-mediated signaling negative regulation of signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication cellular process negative regulation of catabolic process catabolic process macroautophagy negative regulation of metabolic process autophagy regulation of catabolic process regulation of autophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic 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 primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process negative regulation of phosphate metabolic process negative regulation of phosphorus metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process phosphorus metabolic process organelle fusion cellular component organization vacuole fusion organelle organization vacuole organization vacuole fusion, non-autophagic cellular component organization or biogenesis	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 Pho85-Pho80 CDK-cyclin complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle 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 Pho85-Pho80 CDK-cyclin complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

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	IPR013922	Cyclin PHO80-like	Family

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.