3P23

Crystal structure of the Human kinase and RNase domains in complex with ADP

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089781	3002392	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089783	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089781	3002392	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089783	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089781	3002392	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089783	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089781	3002392	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089783	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	Ribonuc_2-5A	e3p23A2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: Ribonuc_2-5A	ECOD (1.6)
A	Pkinase_Tyr	e3p23A1	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: Pkinase_Tyr	ECOD (1.6)
B	Ribonuc_2-5A	e3p23B2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: Ribonuc_2-5A	ECOD (1.6)
B	Pkinase_Tyr	e3p23B1	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: Pkinase_Tyr	ECOD (1.6)
C	Ribonuc_2-5A	e3p23C2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: Ribonuc_2-5A	ECOD (1.6)
C	Pkinase_Tyr	e3p23C1	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: Pkinase_Tyr	ECOD (1.6)
D	Ribonuc_2-5A	e3p23D2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: Ribonuc_2-5A	ECOD (1.6)
D	Pkinase_Tyr	e3p23D1	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: Pkinase_Tyr	ECOD (1.6)

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)
A	1.20.1440.180	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	KEN domain	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)
B	1.20.1440.180	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	KEN domain	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)
C	1.20.1440.180	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	KEN domain	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)
D	1.20.1440.180	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	KEN domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF06479	Ribonuclease 2-5A (Ribonuc_2-5A)	Ribonuclease 2-5A	-	Family
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	Serine/threonine-protein kinase/endoribonuclease IRE1	protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor 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 protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor 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 ADP binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity identical protein binding Hsp90 protein binding heat shock protein binding Hsp70 protein binding protein-folding chaperone binding 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 cation binding magnesium ion binding metal ion binding unfolded protein binding protein homodimerization activity protein dimerization activity protein serine/threonine kinase activity enzyme binding	regulation of biological process catabolic process regulation of cellular process macroautophagy cellular metabolic process biological regulation autophagy regulation of cellular metabolic process regulation of catabolic process regulation of autophagy cellular catabolic process regulation of macroautophagy regulation of cellular catabolic process metabolic process regulation of biological process catabolic process regulation of cellular process macroautophagy cellular metabolic process biological regulation autophagy regulation of cellular metabolic process regulation of catabolic process regulation of autophagy cellular catabolic process regulation of macroautophagy regulation of cellular catabolic process metabolic process cellular process regulation of metabolic process process utilizing autophagic mechanism protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process RNA splicing cellular biosynthetic process RNA metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process mRNA splicing, via endonucleolytic cleavage and ligation RNA splicing, via endonucleolytic cleavage and ligation RNA processing cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus positive regulation of phosphorylation regulation of catalytic activity regulation of signal transduction regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity intracellular signal transduction regulation of primary metabolic process cell communication positive regulation of protein serine/threonine kinase activity positive regulation of metabolic process regulation of phosphate metabolic process intracellular signaling cassette positive regulation of macromolecule metabolic process signal transduction positive regulation of protein phosphorylation positive regulation of MAP kinase activity positive regulation of phosphorus metabolic process positive regulation of MAPK cascade regulation of protein metabolic process positive regulation of intracellular signal transduction positive regulation of JUN kinase activity regulation of MAPK cascade regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of response to stimulus regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation signaling positive regulation of protein metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of response to stimulus positive regulation of molecular function positive regulation of protein modification process regulation of intracellular signal transduction positive regulation of protein kinase activity positive regulation of cellular process regulation of signaling positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of JUN kinase activity MAPK cascade regulation of cell communication regulation of phosphorylation positive regulation of signaling cellular response to topologically incorrect protein cellular response to stress response to stress response to topologically incorrect protein cellular response to unfolded protein response to unfolded protein cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus response to growth factor response to endoplasmic reticulum stress cell population proliferation endothelial cell proliferation epithelial cell proliferation insulin metabolic process homeostatic process response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis response to monosaccharide response to carbohydrate chemical homeostasis response to glucose response to chemical glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus endoplasmic reticulum unfolded protein response IRE1-mediated unfolded protein response regulation of vascular associated smooth muscle cell proliferation positive regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process regulation of biosynthetic process regulation of RNA splicing regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of RNA splicing positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process macromolecule catabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process protein trans-autophosphorylation peptidyl-serine trans-autophosphorylation peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification peptidyl-serine autophosphorylation intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress cell death apoptotic signaling pathway apoptotic process intrinsic apoptotic signaling pathway programmed cell death regulation of cellular response to stress regulation of response to endoplasmic reticulum stress regulation of endoplasmic reticulum unfolded protein response positive regulation of response to endoplasmic reticulum stress regulation of response to stress positive regulation of endoplasmic reticulum unfolded protein response	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle IRE1-TRAF2-ASK1 complex organelle nuclear outer membrane-endoplasmic reticulum membrane network membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle IRE1-TRAF2-ASK1 complex organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane IRE1-RACK1-PP2A complex organelle inner membrane nuclear membrane nucleus organelle envelope nuclear inner membrane nuclear envelope transferase complex endonuclease complex protein kinase complex catalytic complex transferase complex, transferring phosphorus-containing groups endoribonuclease complex Ire1 complex serine/threonine protein kinase complex intracellular protein-containing complex mitochondrion AIP1-IRE1 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018391	Pyrrolo-quinoline quinone beta-propeller repeat	Repeat
A, B, C, D	IPR038357	KEN domain superfamily	Homologous Superfamily
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR045133	Serine/threonine-protein kinase/endoribonuclease IRE1/2-like	Family
A, B, C, D	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
A, B, C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR010513	KEN domain	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
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: O75460	epilepsy pituitary cancer adrenal cortex adenoma Aura cystic fibrosis gastric adenocarcinoma large cell medulloblastoma medulloblastoma ovarian serous adenocarcinoma spina bifida adrenal cortex carcinoma glioblastoma lung adenocarcinoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma epilepsy pituitary cancer adrenal cortex adenoma Aura cystic fibrosis gastric adenocarcinoma large cell medulloblastoma medulloblastoma ovarian serous adenocarcinoma spina bifida adrenal cortex carcinoma glioblastoma lung adenocarcinoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma adrenoleukodystrophy invasive ductal breast carcinoma lung carcinoma ovarian cancer

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.