1YXU | pdb_00001yxu

Crystal Structure of Kinase Pim1 in Complex with AMP

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1yxua_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Proto-oncogene serine/threonine-protein kinase Pim-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1yxub_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Proto-oncogene serine/threonine-protein kinase Pim-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1yxuc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Proto-oncogene serine/threonine-protein kinase Pim-1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1yxud_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Proto-oncogene serine/threonine-protein kinase Pim-1	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	SCOP2B Superfamily	Protein kinase-like (PK-like)	8044193	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8044193	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8044193	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8044193	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	Sigma_1_2	e1yxuA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
B	Sigma_1_2	e1yxuB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
C	Sigma_1_2	e1yxuC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
D	Sigma_1_2	e1yxuD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)

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)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	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)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Proto-oncogene serine/threonine-protein kinase Pim-1	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule 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 cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule 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 purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding transcription factor binding protein binding protein serine/threonine kinase activity enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity ribonucleoprotein complex binding protein-containing complex binding ribosomal small subunit binding ribosome binding	developmental process regulation of stem cell proliferation regulation of biological process cell population proliferation regulation of cellular process cellular developmental process hemopoiesis biological regulation cell development stem cell proliferation regulation of cell population proliferation cell differentiation anatomical structure development hematopoietic stem cell proliferation developmental process regulation of stem cell proliferation regulation of biological process cell population proliferation regulation of cellular process cellular developmental process hemopoiesis biological regulation cell development stem cell proliferation regulation of cell population proliferation cell differentiation anatomical structure development hematopoietic stem cell proliferation regulation of hematopoietic stem cell proliferation cellular process regulation of protein stability regulation of biological quality protein stabilization regulation of mitotic cell cycle cell cycle regulation of cell cycle mitotic cell cycle regulation of localization regulation of transport transport regulation of transmembrane transporter activity establishment of localization transmembrane transport localization regulation of molecular function regulation of transmembrane transport negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death multicellular organismal process regulation of growth positive regulation of cell population proliferation regulation of developmental process regulation of cardiac muscle tissue growth developmental growth cardiac muscle cell proliferation positive regulation of biological process organ growth striated muscle tissue development positive regulation of developmental process multicellular organism development positive regulation of cardiac muscle cell proliferation regulation of organ growth regulation of heart growth regulation of cardiac muscle cell proliferation muscle cell proliferation regulation of multicellular organismal process cardiac muscle tissue growth muscle tissue development positive regulation of developmental growth positive regulation of cellular process positive regulation of heart growth system development striated muscle cell proliferation heart development heart growth regulation of multicellular organismal development regulation of developmental growth cardiac muscle tissue development positive regulation of organ growth growth animal organ development tissue development circulatory system development positive regulation of growth positive regulation of cardiac muscle tissue growth positive regulation of multicellular organismal process regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms negative regulation of response to biotic stimulus response to stimulus regulation of response to external stimulus response to biotic stimulus response to stress regulation of response to stress innate immune response regulation of immune system process response to external biotic stimulus negative regulation of response to stimulus immune response response to other organism defense response regulation of innate immune response negative regulation of immune response defense response to symbiont response to external stimulus regulation of response to stimulus negative regulation of immune system process immune system process defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response negative regulation of innate immune response cellular response to stimulus response to nutrient levels intracellular receptor signaling pathway response to lipid signaling response to vitamin hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to vitamin D cellular response to endogenous stimulus response to vitamin D response to hormone signal transduction cellular response to hormone stimulus response to endogenous stimulus response to nutrient response to oxygen-containing compound cellular response to oxygen-containing compound vitamin D receptor signaling pathway cellular response to nutrient levels cellular response to chemical stimulus cellular response to vitamin response to chemical cellular response to lipid cellular response to nutrient nuclear receptor-mediated signaling pathway positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of cyclin-dependent protein serine/threonine kinase activity regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cyclin-dependent protein kinase activity positive regulation of molecular function positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process positive regulation of cell cycle regulation of phosphorylation positive regulation of cardioblast proliferation positive regulation of cell proliferation involved in heart morphogenesis heart morphogenesis cardioblast proliferation regulation of cardioblast proliferation animal organ morphogenesis animal organ formation heart formation anatomical structure morphogenesis cell proliferation involved in heart morphogenesis anatomical structure formation involved in morphogenesis regulation of cell proliferation involved in heart morphogenesis protein autophosphorylation positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of TORC1 signaling positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of cell communication TORC1 signaling positive regulation of signaling response to type II interferon response to cytokine cellular response to type II interferon response to peptide cellular response to cytokine stimulus fat cell differentiation positive regulation of brown fat cell differentiation positive regulation of fat cell differentiation regulation of cell differentiation regulation of brown fat cell differentiation positive regulation of cell differentiation brown fat cell differentiation regulation of fat cell differentiation cellular detoxification detoxification cellular response to toxic substance response to toxic substance positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol cell periphery plasma membrane membrane nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR017348	Serine/threonine-protein kinase pim-1/2/3	Family
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR051138	PIM Serine/Threonine Kinase	Family
A, B, C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P11309	glioblastoma allergic contact dermatitis prostate intraepithelial neoplasia breast carcinoma giant cell glioblastoma pyelonephritis breast cancer lung cancer Malignant neoplasm of breast ovarian cancer rheumatoid arthritis colorectal adenocarcinoma lung carcinoma malignant pancreatic neoplasm precancerous condition glioblastoma allergic contact dermatitis prostate intraepithelial neoplasia breast carcinoma giant cell glioblastoma pyelonephritis breast cancer lung cancer Malignant neoplasm of breast ovarian cancer rheumatoid arthritis colorectal adenocarcinoma lung carcinoma malignant pancreatic neoplasm precancerous condition atypical teratoid rhabdoid tumor cancer esophageal adenocarcinoma malignant mesothelioma osteosarcoma congenital diaphragmatic hernia cystic fibrosis exocrine pancreatic carcinoma

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.