6F4W | pdb_00006f4w

Crystal structure of H. pylori purine nucleoside phosphorylase in complex with formycin A

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)
F	d6f4wf_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
E	d6f4we_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
D	d6f4wd_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
C	d6f4wc_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
B	d6f4wb_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
A	d6f4wa_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Purine and uridine phosphorylases	8081738	3000626	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Purine and uridine phosphorylases	8081738	3000626	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Purine and uridine phosphorylases	8081738	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8081738	3000626	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8081738	3000626	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8081738	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)
F	SAM_KSR1_N	e6f4wF1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
E	SAM_KSR1_N	e6f4wE1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
D	SAM_KSR1_N	e6f4wD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
C	SAM_KSR1_N	e6f4wC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
B	SAM_KSR1_N	e6f4wB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
A	Ribosomal_S13	e6f4wA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Ribosomal_S13	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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	Purine nucleoside phosphorylase DeoD-type	pentosyltransferase activity glycosyltransferase activity purine-nucleoside phosphorylase activity transferase activity catalytic activity	carbohydrate derivative catabolic 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 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	IPR018016	Nucleoside phosphorylase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR004402	Purine nucleoside phosphorylase DeoD-type	Family
A, B, C, D, E A, B, C, D, E, F	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.