1AKE

STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1akea1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Adenylate kinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1akea2	Small proteins	Rubredoxin-like	Microbial and mitochondrial ADK, insert 'zinc finger' domain	Microbial and mitochondrial ADK, insert 'zinc finger' domain	Microbial and mitochondrial ADK, insert 'zinc finger' domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1akeb1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Adenylate kinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1akeb2	Small proteins	Rubredoxin-like	Microbial and mitochondrial ADK, insert 'zinc finger' domain	Microbial and mitochondrial ADK, insert 'zinc finger' domain	Microbial and mitochondrial ADK, insert 'zinc finger' domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058334	3002021	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058334	3002021	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	Thymidylate_kin	e1akeA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Thymidylate_kin	ECOD (1.6)
A	ADK_lid	e1akeA1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: ADK_lid	ECOD (1.6)
B	Thymidylate_kin	e1akeB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Thymidylate_kin	ECOD (1.6)
B	ADK_lid	e1akeB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: ADK_lid	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00406	Adenylate kinase (ADK)	Adenylate kinase	-	Domain
A, B	PF05191	Adenylate kinase, active site lid (ADK_lid)	Adenylate kinase, active site lid	Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues are resp ...	Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain, is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ADENYLATE KINASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding nucleobase-containing compound kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity transferase activity, transferring phosphorus-containing groups nucleoside monophosphate kinase activity adenylate kinase activity AMP binding	nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside diphosphate biosynthetic process cellular nitrogen compound biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process heterocycle metabolic process phosphate-containing compound metabolic process organic substance biosynthetic process ADP biosynthetic process small molecule metabolic process phosphorus metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside diphosphate biosynthetic process cellular nitrogen compound biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process heterocycle metabolic process phosphate-containing compound metabolic process organic substance biosynthetic process ADP biosynthetic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process cellular metabolic process purine nucleoside diphosphate metabolic process cellular nitrogen compound metabolic process primary metabolic process purine nucleoside diphosphate biosynthetic process nucleotide metabolic process organic cyclic compound metabolic process nucleoside diphosphate metabolic process biosynthetic process aromatic compound biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribonucleoside diphosphate biosynthetic process ribose phosphate metabolic process cellular biosynthetic process nucleoside diphosphate biosynthetic process purine nucleotide metabolic process organic substance metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribonucleoside diphosphate metabolic process nitrogen compound metabolic process carbohydrate derivative biosynthetic process organonitrogen compound metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process cellular process cellular aromatic compound metabolic process nucleoside monophosphate metabolic process purine ribonucleoside monophosphate biosynthetic process purine nucleoside monophosphate biosynthetic process purine nucleoside monophosphate metabolic process cellular metabolic compound salvage purine ribonucleotide salvage AMP biosynthetic process AMP metabolic process nucleotide salvage purine ribonucleoside monophosphate metabolic process ribonucleoside monophosphate metabolic process purine nucleotide salvage AMP salvage purine-containing compound salvage nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process phosphorylation purine ribonucleotide interconversion purine nucleotide interconversion nucleobase-containing small molecule interconversion	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006259	Adenylate kinase subfamily	Family
A, B	IPR007862	Adenylate kinase, active site lid domain	Domain
A, B	IPR000850	Adenylate kinase/UMP-CMP kinase	Family
A, B	IPR033690	Adenylate kinase, conserved site	Conserved Site
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.