3SDM | pdb_00003sdm

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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G	Ribonuc_2-5A	e3sdmG2	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)
G	Pkinase_Tyr	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: Pkinase_Tyr	ECOD (1.6)
F	Ribonuc_2-5A	e3sdmF2	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)
F	Pkinase_Tyr	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: Pkinase_Tyr	ECOD (1.6)
E	Ribonuc_2-5A	e3sdmE2	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)
E	Pkinase_Tyr	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: Pkinase_Tyr	ECOD (1.6)
D	Ribonuc_2-5A	e3sdmD2	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	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: Pkinase_Tyr	ECOD (1.6)
C	Ribonuc_2-5A	e3sdmC2	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	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: Pkinase_Tyr	ECOD (1.6)
B	Ribonuc_2-5A	e3sdmB2	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	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: Pkinase_Tyr	ECOD (1.6)
A	Ribonuc_2-5A	e3sdmA2	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	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: Pkinase_Tyr	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
A, B, C, D, E A, B, C, D, E, F, G	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, 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 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 catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity cation binding metal ion binding identical protein binding	polyol metabolic process inositol metabolic process alcohol metabolic process small molecule metabolic process metabolic process cellular 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 component organization or biogenesis external encapsulating structure organization cellular response to stimulus polyol metabolic process inositol metabolic process alcohol metabolic process small molecule metabolic process metabolic process cellular 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 component organization or biogenesis external encapsulating structure organization cellular response to stimulus regulation of biological process cellular response to topologically incorrect protein regulation of cellular process response to stimulus signaling biological regulation endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein intracellular signal transduction cell communication cellular response to stress response to stress response to topologically incorrect protein IRE1-mediated unfolded protein response signal transduction response to endoplasmic reticulum stress RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process macromolecule metabolic process RNA processing localization protein localization to Golgi apparatus protein localization to organelle macromolecule localization intracellular protein localization intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress cell death apoptotic signaling pathway apoptotic process intrinsic apoptotic signaling pathway programmed cell death	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 cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane 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 cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment membrane 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 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.