4W5J | pdb_00004w5j

New structural conformations of adenylate kinase from Streptococcus pneumoniae D39 with Ap5A

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Cytidylate_kin_2	e4w5jD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cytidylate_kin_2	ECOD (1.6)
D	ADK_lid	e4w5jD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: ADK_lid	ECOD (1.6)
C	Cytidylate_kin_2	e4w5jC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cytidylate_kin_2	ECOD (1.6)
C	ADK_lid	e4w5jC1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: ADK_lid	ECOD (1.6)
B	Cytidylate_kin_2	e4w5jB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cytidylate_kin_2	ECOD (1.6)
B	ADK_lid	e4w5jB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: ADK_lid	ECOD (1.6)
A	Cytidylate_kin_2	e4w5jA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cytidylate_kin_2	ECOD (1.6)
A	ADK_lid	e4w5jA1	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)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	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)
A	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, C, D	PF00406	Adenylate kinase (ADK)	Adenylate kinase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Adenylate kinase	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 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	ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process AMP metabolic process nucleobase-containing compound metabolic process nucleotide salvage metabolic compound salvage ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process AMP metabolic process nucleobase-containing compound metabolic process nucleotide salvage metabolic compound salvage ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process purine nucleotide salvage AMP salvage small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine-containing compound salvage primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process purine-containing compound metabolic process biosynthetic process purine ribonucleotide salvage organophosphate metabolic process organophosphate biosynthetic process AMP biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine ribonucleotide metabolic process ribonucleoside monophosphate biosynthetic process purine nucleotide biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006259	Adenylate kinase subfamily	Family
A, B, C, D	IPR000850	Adenylate kinase/UMP-CMP kinase	Family
A, B, C, D	IPR033690	Adenylate kinase, conserved site	Conserved Site
A, B, C, D	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.