2QRD | pdb_00002qrd

Crystal Structure of the Adenylate Sensor from AMP-activated Protein Kinase in complex with ADP and ATP

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)
F [auth E]	d2qrde1	Alpha and beta proteins (a+b)	CBS-domain pair	CBS-domain pair	CBS-domain pair	automated matches	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
F [auth E]	d2qrde3	Artifacts	Tags	Tags	Tags	N-terminal Tags	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
C [auth G]	d2qrdg1	Alpha and beta proteins (a+b)	CBS-domain pair	CBS-domain pair	CBS-domain pair	automated matches	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
C [auth G]	d2qrdg3	Artifacts	Tags	Tags	Tags	N-terminal Tags	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
E [auth D]	d2qrdd_	Alpha and beta proteins (a+b)	AMPKBI-like	AMPKBI-like	AMPKBI-like	automated matches	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
B	d2qrdb_	Alpha and beta proteins (a+b)	AMPKBI-like	AMPKBI-like	AMPKBI-like	automated matches	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
D [auth C]	d2qrdc_	Alpha and beta proteins (a+b)	TBP-like	KA1-like	Ssp2 C-terminal domain-like	Snf1-like protein kinase ssp2	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
A	d2qrda_	Alpha and beta proteins (a+b)	TBP-like	KA1-like	Ssp2 C-terminal domain-like	Snf1-like protein kinase ssp2	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth E]	SCOP2B Superfamily	CBS-domain pair	8035215	3000123	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	CBS-domain pair	8035214	3000123	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	CBS-domain pair	8035214	3000123	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	CBS-domain pair	8035215	3000123	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	AMPKBI-like	8036351	3000446	SCOP2B (2022-06-29)
B	SCOP2 Family	AMPKBI-like	8023972	4001835	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	AMPKBI-like	8036351	3000446	SCOP2 (2022-06-29)
D [auth C]	SCOP2B Superfamily	KA1-like	8036350	3001856	SCOP2B (2022-06-29)
A	SCOP2 Family	Ssp2 C-terminal domain-like	8023971	4002378	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	KA1-like	8036350	3001856	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth E]	Rpf1_C	e2qrdE1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (develop294)
C [auth G]	Rpf1_C	e2qrdG2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (develop294)
C [auth G]	Pneumovirus_M2	e2qrdG3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Pneumovirus_M2	ECOD (develop294)
E [auth D]	RimK	e2qrdD2	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: RimK	ECOD (develop294)
B	RimK	e2qrdB2	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: RimK	ECOD (develop294)
D [auth C]	Glyco_hydro_18	e2qrdC1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Glyco_hydro_18	ECOD (develop294)
A	AdenylateSensor	e2qrdA1	A: a+b two layers	X: TBP-like	H: Kinase associated domain 1, KA1	T: Kinase associated domain 1, KA1	F: AdenylateSensor	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth E]	3.10.580.10	Alpha Beta	Roll	CBS-domain	CBS-domain	CATH (4.3.0)
C [auth G]	3.10.580.10	Alpha Beta	Roll	CBS-domain	CBS-domain	CATH (4.3.0)
E [auth D]	2.20.25.290	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
B	2.20.25.290	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
D [auth C]	3.30.310.80	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	Kinase associated domain 1, KA1	CATH (4.3.0)
A	3.30.310.80	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	Kinase associated domain 1, KA1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth G], F [auth E]	PF00571	CBS domain (CBS)	CBS domain	CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands ...	CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet [5]. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet [4]. CBS domain pairs from AMPK bind AMP or ATP [5]. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP [5].	Domain
B, E [auth D]	PF04739	5'-AMP-activated protein kinase beta subunit, interaction domain (AMPKBI)	5'-AMP-activated protein kinase beta subunit, interaction domain	-	Family
A, D [auth C]	PF16579	Adenylate sensor of SNF1-like protein kinase (AdenylateSensor)	Adenylate sensor of SNF1-like protein kinase	AdenylateSensor is a family found at the C-terminus of SNF1-like protein kinases snf other protein-kinases [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth G], F [auth E]	Protein C1556.08c	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 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 ADP binding protein binding kinase binding enzyme binding protein kinase binding enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity kinase activator activity enzyme activator activity molecular function activator activity protein kinase activator activity cation binding AMP binding	monosaccharide metabolic process regulation of cellular process positive regulation of biological process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis regulation of biosynthetic process monosaccharide metabolic process regulation of cellular process positive regulation of biological process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process biosynthetic process regulation of gluconeogenesis metabolic process cellular process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process regulation of metabolic process glucose metabolic process response to nutrient levels carbon utilization regulation of response to nutrient levels response to stimulus regulation of response to stimulus regulation of carbon utilization cellular response to stimulus cellular response to nutrient levels cellular response to stress response to stress response to starvation cellular response to glucose starvation cellular response to starvation sexual reproduction regulation of reproductive process reproductive process regulation of conjugation with cellular fusion conjugation with cellular fusion induction of conjugation with cellular fusion positive regulation of conjugation with cellular fusion positive regulation of reproductive process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process regulation of ATP metabolic process regulation of purine nucleotide catabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process regulation of carbohydrate catabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process signaling signal transduction cell communication	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex intracellular protein-containing complex nucleotide-activated protein kinase complex membrane-bounded organelle intracellular organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex intracellular protein-containing complex nucleotide-activated protein kinase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B, E [auth D]	SPCC1919.03c protein	protein binding binding kinase binding enzyme binding protein kinase binding enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	regulation of biological process regulation of cellular process flocculation positive regulation of cell adhesion regulation of cell adhesion biological process involved in intraspecies interaction between organisms biological regulation positive regulation of biological process positive regulation of cell-cell adhesion positive regulation of flocculation cell adhesion cell-cell adhesion regulation of cell-cell adhesion cellular process regulation of biological process regulation of cellular process flocculation positive regulation of cell adhesion regulation of cell adhesion biological process involved in intraspecies interaction between organisms biological regulation positive regulation of biological process positive regulation of cell-cell adhesion positive regulation of flocculation cell adhesion cell-cell adhesion regulation of cell-cell adhesion cellular process regulation of flocculation adhesion between unicellular organisms positive regulation of cellular process sexual reproduction regulation of reproductive process reproductive process regulation of conjugation with cellular fusion conjugation with cellular fusion induction of conjugation with cellular fusion positive regulation of conjugation with cellular fusion positive regulation of reproductive process cellular response to stimulus response to stimulus signaling intracellular signal transduction cell communication calcium-mediated signaling intracellular signaling cassette signal transduction CAMKK-AMPK signaling cascade	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex intracellular protein-containing complex nucleotide-activated protein kinase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex intracellular protein-containing complex nucleotide-activated protein kinase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
A, D [auth C]	SNF1-like protein kinase ssp2	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 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 catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process translation gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of cytoplasmic translation negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process cytoplasmic translation metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of cytoplasmic translation regulation of metabolic process cell cycle switching sexual reproduction positive regulation of cell cycle switching, mitotic to meiotic cell cycle regulation of reproductive process reproductive process positive regulation of biological process negative regulation of cell cycle negative regulation of mitotic cell cycle mitotic cell cycle regulation of mitotic cell cycle regulation of cell cycle switching, mitotic to meiotic cell cycle positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process positive regulation of reproductive process regulation of meiotic cell cycle regulation of cell cycle process meiotic cell cycle positive regulation of meiotic cell cycle positive regulation of cell cycle cell cycle switching, mitotic to meiotic cell cycle cellular response to stimulus response to stimulus cellular response to sterol depletion signaling response to sterol depletion intracellular signal transduction cell communication SREBP signaling pathway cellular response to stress response to stress ER-nucleus signaling pathway signal transduction regulation of conjugation with cellular fusion conjugation with cellular fusion induction of conjugation with cellular fusion positive regulation of conjugation with cellular fusion negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction negative regulation of cell communication negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling calcium-mediated signaling intracellular signaling cassette CAMKK-AMPK signaling cascade 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 positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex intracellular protein-containing complex nucleotide-activated protein kinase complex intracellular membraneless organelle intracellular organelle microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex intracellular protein-containing complex nucleotide-activated protein kinase complex intracellular membraneless organelle intracellular organelle microtubule organizing center cytoskeleton organelle membraneless organelle spindle pole body microtubule cytoskeleton mitotic spindle pole body membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth G], F [auth E]	IPR046342	CBS domain superfamily	Homologous Superfamily
C [auth G], F [auth E]	IPR050511	AMP-activated protein kinase gamma/SDS23 families	Family
C [auth G], F [auth E]	IPR000644	CBS domain	Domain
B, E [auth D]	IPR032640	AMP-activated protein kinase, glycogen-binding domain	Domain
B, E [auth D]	IPR037256	ASC domain superfamily	Homologous Superfamily
B, E [auth D]	IPR006828	Association with the SNF1 complex (ASC) domain	Domain
B, E [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, E [auth D]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B, E [auth D]	IPR050827	CRP1/MDG1 DNA-binding & kinase subunit	Family
A, D [auth C]	IPR028375	KA1 domain/Ssp2, C-terminal	Homologous Superfamily
A, D [auth C]	IPR017441	Protein kinase, ATP binding site	Binding Site
A, D [auth C]	IPR013896	Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain	Domain
A, D [auth C]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, D [auth C]	IPR032270	AMPK, C-terminal adenylate sensor domain	Domain
A, D [auth C]	IPR000719	Protein kinase domain	Domain
A, D [auth C]	IPR015940	Ubiquitin-associated domain	Domain
A, D [auth C]	IPR008271	Serine/threonine-protein kinase, active site	Active Site

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.