6W1I | pdb_00006w1i

Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	d6w1id1	Alpha and beta proteins (a/b)	PRTase-like	PRTase-like	Phosphoribosyltransferases (PRTases)	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
D	d6w1id2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
C	d6w1ic1	Alpha and beta proteins (a/b)	PRTase-like	PRTase-like	Phosphoribosyltransferases (PRTases)	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
C	d6w1ic2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d6w1ib1	Alpha and beta proteins (a/b)	PRTase-like	PRTase-like	Phosphoribosyltransferases (PRTases)	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d6w1ib2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
A	d6w1ia1	Alpha and beta proteins (a/b)	PRTase-like	PRTase-like	Phosphoribosyltransferases (PRTases)	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
A	d6w1ia2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PRTase-like	8033980	3000060	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PRTase-like	8033980	3000060	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PRTase-like	8033980	3000060	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PRTase-like	8033980	3000060	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)
D	Pro_isomerase	e6w1iD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
C	Pro_isomerase	e6w1iC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
B	CSD	e6w1iB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: CSD	ECOD (v294.1)
A	Pro_isomerase	e6w1iA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00156	Phosphoribosyl transferase domain (Pribosyltran)	Phosphoribosyl transferase domain	This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyl-transferase EC:2.4.2.7, Swiss:P07672. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase Swiss:P51900. Hypoxanthine phosph ...	This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyl-transferase EC:2.4.2.7, Swiss:P07672. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase Swiss:P51900. Hypoxanthine phosphoribosyl-transferase EC:2.4.2.8 Swiss:P36766. Ribose-phosphate pyrophosphokinase i EC:2.7.6.1 Swiss:P09329. Amidophosphoribosyltransferase EC:2.4.2.14 Swiss:P00496. Orotate phosphoribosyl-transferase EC:2.4.2.10 Swiss:P11172. Uracil phosphoribosyl-transferase EC:2.4.2.9 Swiss:P25532. Xanthine-guanine phosphoribosyl-transferase EC:2.4.2.22 Swiss:P00501. In Arabidopsis, At the very N-terminus of this domain is the P-Loop NTPase domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Xanthine phosphoribosyltransferase	pentosyltransferase activity glycosyltransferase activity purine phosphoribosyltransferase activity xanthine phosphoribosyltransferase activity transferase activity catalytic activity	ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic 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 ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic 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 small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process XMP metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process XMP salvage 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 XMP biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine ribonucleotide metabolic process ribonucleoside monophosphate biosynthetic process purine nucleotide biosynthetic process nucleoside biosynthetic process purine ribonucleoside metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process nucleoside salvage purine ribonucleoside biosynthetic process ribonucleoside biosynthetic process nucleoside metabolic process nucleobase-containing small molecule biosynthetic process purine ribonucleoside salvage purine nucleoside biosynthetic process purine nucleoside metabolic process ribonucleoside metabolic process purine nucleobase metabolic process nucleobase metabolic process xanthine metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR010079	Xanthine phosphoribosyltransferase	Family
A, B, C, D	IPR000836	Phosphoribosyltransferase domain	Domain
A, B, C, D	IPR029057	Phosphoribosyltransferase-like	Homologous Superfamily
A, B, C, D	IPR050118	Purine/Pyrimidine Phosphoribosyltransferase	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.