1YXB | pdb_00001yxb

Crystal structure of Phosphoribosyl-ATP pyrophosphatase from Streptomyces coelicolor. NESG target RR8.

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)
B	d1yxbb2	All alpha proteins	all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	HisE-like (PRA-PH)	Phosphoribosyl-ATP pyrophosphatase HisE	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
B	d1yxbb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
D	d1yxbd2	All alpha proteins	all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	HisE-like (PRA-PH)	Phosphoribosyl-ATP pyrophosphatase HisE	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
D	d1yxbd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
E	d1yxbe2	All alpha proteins	all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	HisE-like (PRA-PH)	Phosphoribosyl-ATP pyrophosphatase HisE	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
E	d1yxbe3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
F	d1yxbf2	All alpha proteins	all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	HisE-like (PRA-PH)	Phosphoribosyl-ATP pyrophosphatase HisE	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
F	d1yxbf3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
G	d1yxbg2	All alpha proteins	all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	HisE-like (PRA-PH)	Phosphoribosyl-ATP pyrophosphatase HisE	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
G	d1yxbg3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
A	d1yxba1	All alpha proteins	all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	HisE-like (PRA-PH)	Phosphoribosyl-ATP pyrophosphatase HisE	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
A	d1yxba2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
C	d1yxbc2	All alpha proteins	all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	HisE-like (PRA-PH)	Phosphoribosyl-ATP pyrophosphatase HisE	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
C	d1yxbc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
H	d1yxbh2	All alpha proteins	all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	HisE-like (PRA-PH)	Phosphoribosyl-ATP pyrophosphatase HisE	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)
H	d1yxbh3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor ) [TaxId: 1902 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	all-alpha NTP pyrophosphatases	8035010	3001174	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	all-alpha NTP pyrophosphatases	8035010	3001174	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	all-alpha NTP pyrophosphatases	8035010	3001174	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	all-alpha NTP pyrophosphatases	8035010	3001174	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	all-alpha NTP pyrophosphatases	8035010	3001174	SCOP2B (2022-06-29)
A	SCOP2 Family	HisE-like	8022630	4001521	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	all-alpha NTP pyrophosphatases	8035010	3001174	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	all-alpha NTP pyrophosphatases	8035010	3001174	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	all-alpha NTP pyrophosphatases	8035010	3001174	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	PRA-PH_1	e1yxbB1	A: alpha bundles	X: all-alpha NTP pyrophosphatases (From Homology)	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PRA-PH_1	ECOD (1.6)
D	PRA-PH_1	e1yxbD1	A: alpha bundles	X: all-alpha NTP pyrophosphatases (From Homology)	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PRA-PH_1	ECOD (1.6)
E	PRA-PH_1	e1yxbE1	A: alpha bundles	X: all-alpha NTP pyrophosphatases (From Homology)	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PRA-PH_1	ECOD (1.6)
F	PRA-PH_1	e1yxbF1	A: alpha bundles	X: all-alpha NTP pyrophosphatases (From Homology)	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PRA-PH_1	ECOD (1.6)
G	PRA-PH_1	e1yxbG1	A: alpha bundles	X: all-alpha NTP pyrophosphatases (From Homology)	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PRA-PH_1	ECOD (1.6)
A	PRA-PH_1	e1yxbA1	A: alpha bundles	X: all-alpha NTP pyrophosphatases (From Homology)	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PRA-PH_1	ECOD (1.6)
C	PRA-PH_1	e1yxbC1	A: alpha bundles	X: all-alpha NTP pyrophosphatases (From Homology)	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PRA-PH_1	ECOD (1.6)
H	PRA-PH_1	e1yxbH1	A: alpha bundles	X: all-alpha NTP pyrophosphatases (From Homology)	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PRA-PH_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.287.1080	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	MazG-like	CATH (4.3.0)
D	1.10.287.1080	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	MazG-like	CATH (4.3.0)
E	1.10.287.1080	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	MazG-like	CATH (4.3.0)
F	1.10.287.1080	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	MazG-like	CATH (4.3.0)
G	1.10.287.1080	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	MazG-like	CATH (4.3.0)
A	1.10.287.1080	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	MazG-like	CATH (4.3.0)
C	1.10.287.1080	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	MazG-like	CATH (4.3.0)
H	1.10.287.1080	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	MazG-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF01503	Phosphoribosyl-ATP pyrophosphohydrolase (PRA-PH)	Phosphoribosyl-ATP pyrophosphohydrolase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Phosphoribosyl-ATP pyrophosphatase	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 pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity phosphoribosyl-ATP diphosphatase activity	oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process imidazole-containing compound metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process aromatic amino acid metabolic process aromatic amino acid family biosynthetic process L-histidine metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process imidazole-containing compound metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process aromatic amino acid metabolic process aromatic amino acid family biosynthetic process L-histidine metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process L-histidine biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR021130	Phosphoribosyl-ATP pyrophosphohydrolase-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008179	Phosphoribosyl-ATP pyrophosphohydrolase	Family

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.