7APU | pdb_00007apu

Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058334	3002021	SCOP2B (2022-06-29)
A	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)
B	Ribosomal_L19	e7apuB1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (develop294)
A	Ribosomal_L27A, PF29471	e7apuA1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L27A, PF29471	ECOD (develop294)

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 nucleobase-containing compound kinase activity nucleoside monophosphate kinase activity kinase activity AMP kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleobase-containing compound kinase activity nucleoside monophosphate kinase activity kinase activity AMP kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding nucleoside diphosphate kinase activity AMP binding	ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside diphosphate biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process nucleoside diphosphate biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process ribonucleoside diphosphate metabolic process ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside diphosphate biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process nucleoside diphosphate biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process ribonucleoside diphosphate metabolic process ADP biosynthetic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside diphosphate metabolic process primary metabolic process purine nucleoside diphosphate biosynthetic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process ADP metabolic process nucleoside diphosphate metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process purine ribonucleoside diphosphate metabolic process metabolic process cellular process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribonucleoside diphosphate biosynthetic process nucleoside monophosphate metabolic process purine ribonucleoside monophosphate biosynthetic process AMP metabolic process nucleotide salvage metabolic compound salvage purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleoside monophosphate metabolic process purine nucleotide salvage AMP salvage purine-containing compound salvage nucleoside monophosphate biosynthetic process purine ribonucleotide salvage AMP biosynthetic process ribonucleoside monophosphate biosynthetic process purine nucleobase metabolic process nucleobase metabolic process adenine metabolic process purine ribonucleotide interconversion purine nucleotide interconversion nucleobase-containing small molecule interconversion	cellular anatomical structure intracellular anatomical structure cytoplasm 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 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.