3OF3 | pdb_00003of3

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae

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)
A	d3of3a_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d3of3b_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
C	d3of3c_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
D	d3of3d_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
E	d3of3e_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
F	d3of3f_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
G	d3of3g_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
H	d3of3h_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
I	d3of3i_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
J	d3of3j_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
K	d3of3k_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
L	d3of3l_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	3000626	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Purine and uridine phosphorylases	8035830	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)
A	PNP_UDP_1	e3of3A1	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	e3of3B1	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	e3of3C1	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	e3of3D1	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	e3of3E1	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	e3of3F1	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	e3of3G1	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	e3of3H1	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	e3of3I1	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	e3of3J1	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	e3of3K1	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	e3of3L1	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)
A	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)
C	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)
E	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)
G	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)
I	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)
K	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)

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	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	Purine nucleoside phosphorylase deoD-type 1	pentosyltransferase activity glycosyltransferase activity purine-nucleoside phosphorylase activity transferase activity catalytic activity	carbohydrate derivative catabolic process glycosyl compound metabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule catabolic process nucleobase-containing small molecule metabolic process nucleoside catabolic process carbohydrate derivative catabolic process glycosyl compound metabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule catabolic process nucleobase-containing small molecule metabolic process nucleoside catabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process purine nucleoside metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	IPR018016	Nucleoside phosphorylase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR004402	Purine nucleoside phosphorylase DeoD-type	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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.