1RXU | pdb_00001rxu

E. coli uridine phosphorylase: thymidine phosphate complex

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)
R	d1rxur_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
Q	d1rxuq_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
P	d1rxup_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
O	d1rxuo_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
N	d1rxun_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
M	d1rxum_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d1rxul_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d1rxuk_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d1rxuj_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d1rxui_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1rxuh_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1rxug_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1rxuf_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1rxue_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1rxud_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1rxuc_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1rxub_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1rxua_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
R	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	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)
R	PNP_UDP_1	e1rxuR1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
Q	PNP_UDP_1	e1rxuQ1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
P	PNP_UDP_1	e1rxuP1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
O	PNP_UDP_1	e1rxuO1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
N	PNP_UDP_1	e1rxuN1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
M	PNP_UDP_1	e1rxuM1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
L	PNP_UDP_1	e1rxuL1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
K	PNP_UDP_1	e1rxuK1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
J	PNP_UDP_1	e1rxuJ1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
I	PNP_UDP_1	e1rxuI1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
H	PNP_UDP_1	e1rxuH1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
G	PNP_UDP_1	e1rxuG1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
F	PNP_UDP_1	e1rxuF1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
E	PNP_UDP_1	e1rxuE1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
D	PNP_UDP_1	e1rxuD1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
C	PNP_UDP_1	e1rxuC1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
B	PNP_UDP_1	e1rxuB1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
A	PNP_UDP_1	e1rxuA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
R	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
Q	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
P	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
O	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
N	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
M	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
L	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
K	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
J	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
I	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
H	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
G	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
F	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
E	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
D	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
C	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
B	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
A	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	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, I, J, K, L, M, N, O, P, Q, R	PF01048	Phosphorylase superfamily (PNP_UDP_1)	Phosphorylase superfamily	Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)	Domain

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, I, J, K, L, M, N, O, P, Q, R	Uridine phosphorylase	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 cation binding potassium ion binding alkali metal ion binding metal ion binding pentosyltransferase activity glycosyltransferase activity uridine phosphorylase activity transferase activity catalytic activity pyrimidine-nucleoside phosphorylase activity identical protein binding protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process uridine metabolic process pyrimidine nucleoside metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process uridine metabolic process pyrimidine nucleoside metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside catabolic process primary metabolic process glycosyl compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process uridine catabolic process pyrimidine ribonucleoside metabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process metabolic process pyrimidine ribonucleoside catabolic process small molecule catabolic process ribonucleoside catabolic process ribonucleoside metabolic process ribose phosphate metabolic process nucleotide biosynthetic process pyrimidine ribonucleotide salvage pyrimidine nucleotide metabolic process pyrimidine-containing compound salvage pyrimidine nucleotide salvage nucleotide salvage metabolic compound salvage ribonucleotide biosynthetic process UMP salvage UMP biosynthetic process ribonucleotide metabolic process phosphate-containing compound metabolic process UMP metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process pyrimidine ribonucleotide catabolic process ribonucleotide catabolic process pyrimidine ribonucleoside monophosphate catabolic process organophosphate catabolic process nucleoside phosphate catabolic process pyrimidine nucleotide catabolic process ribonucleoside monophosphate catabolic process nucleotide catabolic process pyrimidine nucleoside monophosphate catabolic process nucleoside monophosphate catabolic process UMP catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR010058	Uridine phosphorylase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR018016	Nucleoside phosphorylase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR000845	Nucleoside phosphorylase domain	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.