5DED | pdb_00005ded

Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp

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)
H	d5dedh_	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RelA/SpoT domain	automated matches	(Bacillus subtilis PY79 ) [TaxId: 1415167 ],	SCOPe (2.08)
G	d5dedg_	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RelA/SpoT domain	automated matches	(Bacillus subtilis PY79 ) [TaxId: 1415167 ],	SCOPe (2.08)
F	d5dedf_	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RelA/SpoT domain	automated matches	(Bacillus subtilis PY79 ) [TaxId: 1415167 ],	SCOPe (2.08)
E	d5dede_	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RelA/SpoT domain	automated matches	(Bacillus subtilis PY79 ) [TaxId: 1415167 ],	SCOPe (2.08)
D [auth C]	d5dedc_	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RelA/SpoT domain	automated matches	(Bacillus subtilis PY79 ) [TaxId: 1415167 ],	SCOPe (2.08)
C [auth B]	d5dedb_	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RelA/SpoT domain	automated matches	(Bacillus subtilis PY79 ) [TaxId: 1415167 ],	SCOPe (2.08)
B [auth A]	d5deda_	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RelA/SpoT domain	automated matches	(Bacillus subtilis PY79 ) [TaxId: 1415167 ],	SCOPe (2.08)
A [auth D]	d5dedd_	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RelA/SpoT domain	automated matches	(Bacillus subtilis PY79 ) [TaxId: 1415167 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Nucleotidyltransferase-like	8058788	3000129	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nucleotidyltransferase-like	8058788	3000129	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleotidyltransferase-like	8058788	3000129	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleotidyltransferase-like	8058788	3000129	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Nucleotidyltransferase-like	8058788	3000129	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Nucleotidyltransferase-like	8058788	3000129	SCOP2B (2022-06-29)
B [auth A]	SCOP2 Family	RelA/SpoT domain	8058787	4001424	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Nucleotidyltransferase-like	8058788	3000129	SCOP2 (2022-06-29)
A [auth D]	SCOP2B Superfamily	Nucleotidyltransferase-like	8058788	3000129	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)
H	Glyco_transf_41	e5dedH1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: Glyco_transf_41	ECOD (v294.1)
G	Glyco_transf_41	e5dedG1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: Glyco_transf_41	ECOD (v294.1)
F	Glyco_transf_41	e5dedF1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: Glyco_transf_41	ECOD (v294.1)
E	Glyco_transf_41	e5dedE1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: Glyco_transf_41	ECOD (v294.1)
D [auth C]	Glyco_transf_41	e5dedC1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: Glyco_transf_41	ECOD (v294.1)
C [auth B]	Glyco_transf_41	e5dedB1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: Glyco_transf_41	ECOD (v294.1)
B [auth A]	Glyco_transf_41	e5dedA1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: Glyco_transf_41	ECOD (v294.1)
A [auth D]	Glyco_transf_41	e5dedD1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: Glyco_transf_41	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
H	1.10.287.860	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Nucleotidyltransferase	CATH (4.3.0)
G	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
G	1.10.287.860	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Nucleotidyltransferase	CATH (4.3.0)
F	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
F	1.10.287.860	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Nucleotidyltransferase	CATH (4.3.0)
E	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
E	1.10.287.860	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Nucleotidyltransferase	CATH (4.3.0)
D [auth C]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
D [auth C]	1.10.287.860	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Nucleotidyltransferase	CATH (4.3.0)
C [auth B]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
C [auth B]	1.10.287.860	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Nucleotidyltransferase	CATH (4.3.0)
B [auth A]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
B [auth A]	1.10.287.860	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Nucleotidyltransferase	CATH (4.3.0)
A [auth D]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A [auth D]	1.10.287.860	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Nucleotidyltransferase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H	PF04607	Region found in RelA / SpoT proteins (RelA_SpoT)	Region found in RelA / SpoT proteins	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H	GTP pyrophosphokinase YjbM	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 kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups GTP diphosphokinase activity diphosphotransferase activity guanyl nucleotide binding GTP binding guanyl ribonucleotide binding cation binding metal ion binding	ribose phosphate metabolic process nucleoside bisphosphate metabolic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process ribonucleoside bisphosphate metabolic process guanosine tetraphosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside bisphosphate metabolic process purine ribonucleoside bisphosphate biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process guanosine tetraphosphate metabolic process ribose phosphate metabolic process nucleoside bisphosphate metabolic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process ribonucleoside bisphosphate metabolic process guanosine tetraphosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside bisphosphate metabolic process purine ribonucleoside bisphosphate biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process guanosine tetraphosphate metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process small molecule metabolic process purine nucleoside bisphosphate biosynthetic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleoside bisphosphate biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine ribonucleotide metabolic process purine nucleotide biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H	IPR052366	GTP Pyrophosphokinase	Family
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H	IPR007685	RelA/SpoT	Domain

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.