3SDM

Structure of oligomeric kinase/RNase Ire1 in complex with an oligonucleotide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089777	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089775	3002392	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089775	3002392	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089777	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089775	3002392	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089777	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089775	3002392	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089777	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089775	3002392	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089777	3000066	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089775	3002392	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089777	3000066	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ire1-RNaseL RNase domain-like	8089775	3002392	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Protein kinase-like (PK-like)	8089777	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)
D	PF06479	e3sdmD2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: PF06479	ECOD (1.6)
D	PF00069	e3sdmD1	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: PF00069	ECOD (1.6)
F	PF06479	e3sdmF2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: PF06479	ECOD (1.6)
F	PF00069	e3sdmF1	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: PF00069	ECOD (1.6)
A	PF06479	e3sdmA2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: PF06479	ECOD (1.6)
A	PF00069	e3sdmA1	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: PF00069	ECOD (1.6)
B	PF06479	e3sdmB2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: PF06479	ECOD (1.6)
B	PF00069	e3sdmB1	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: PF00069	ECOD (1.6)
C	PF06479	e3sdmC2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: PF06479	ECOD (1.6)
C	PF00069	e3sdmC1	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: PF00069	ECOD (1.6)
E	PF06479	e3sdmE2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: PF06479	ECOD (1.6)
E	PF00069	e3sdmE1	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: PF00069	ECOD (1.6)
G	PF06479	e3sdmG2	A: alpha bundles	X: Four-helical up-and-down bundle	H: HEPN	T: Nucleotidyltransferase substrate binding subunit/domain	F: PF06479	ECOD (1.6)
G	PF00069	e3sdmG1	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: PF00069	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G	PF06479	Ribonuclease 2-5A (Ribonuc_2-5A)	Ribonuclease 2-5A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G	Serine/threonine-protein kinase/endoribonuclease IRE1	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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding unfolded protein binding protein binding protein serine/threonine kinase activity 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 cation binding metal ion binding identical protein binding	polyol metabolic process organic substance metabolic process inositol metabolic process organic hydroxy compound metabolic process alcohol metabolic process small molecule metabolic process metabolic process fungal-type cell wall organization cellular component organization fungal-type cell wall organization or biogenesis cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis polyol metabolic process organic substance metabolic process inositol metabolic process organic hydroxy compound metabolic process alcohol metabolic process small molecule metabolic process metabolic process fungal-type cell wall organization cellular component organization fungal-type cell wall organization or biogenesis cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization cellular response to stimulus regulation of biological process response to organic substance regulation of cellular process cellular response to topologically incorrect protein response to stimulus signaling biological regulation endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein cell communication cellular response to chemical stimulus cellular response to stress response to chemical response to stress response to topologically incorrect protein IRE1-mediated unfolded protein response signal transduction cellular response to organic substance response to endoplasmic reticulum stress cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process biosynthetic process organic substance biosynthetic process macromolecule metabolic process RNA processing protein localization localization cellular localization protein localization to Golgi apparatus protein localization to organelle cellular macromolecule localization macromolecule localization phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure membrane protein complex transferase complex endomembrane system endonuclease complex protein kinase complex endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex membrane-bounded organelle protein-containing complex intracellular anatomical structure membrane protein complex transferase complex endomembrane system endonuclease complex protein kinase complex endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment membrane cellular anatomical entity intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups endoribonuclease complex Ire1 complex organelle endoplasmic reticulum serine/threonine protein kinase complex cytoplasm organelle membrane intracellular protein-containing complex IRE1-TRAF2-ASK1 complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR018391	Pyrrolo-quinoline quinone beta-propeller repeat	Repeat
A, B, C, D, E A, B, C, D, E, F, G	IPR038357	KEN domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR045133	Serine/threonine-protein kinase/endoribonuclease IRE1/2-like	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR000719	Protein kinase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR010513	KEN domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F, G	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
A, B, C, D, E A, B, C, D, E, F, G	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 National Science Foundation (DBI-1832184), 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.