4GKA | pdb_00004gka

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with phosphate

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d4gkaf_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4gkae_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4gkad_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4gkac_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4gkab_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4gkaa_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	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	8039220	3000626	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Purine and uridine phosphorylases	8039220	3000626	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Purine and uridine phosphorylases	8039220	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8039220	3000626	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8039220	3000626	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8039220	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	tRNA_synthFbeta	e4gkaF2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: tRNA_synthFbeta	ECOD (v294.1)
E	tRNA_synthFbeta	e4gkaE2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: tRNA_synthFbeta	ECOD (v294.1)
D	ClpB_D2-small	e4gkaD1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: ClpB_D2-small	ECOD (v294.1)
C	tRNA_synthFbeta	e4gkaC2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: tRNA_synthFbeta	ECOD (v294.1)
B	ClpB_D2-small	e4gkaB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: ClpB_D2-small	ECOD (v294.1)
A	ClpB_D2-small	e4gkaA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: ClpB_D2-small	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	binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding ion binding anion binding phosphate ion binding guanosine phosphorylase activity pentosyltransferase activity glycosyltransferase activity purine-nucleoside phosphorylase activity transferase activity catalytic activity binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding ion binding anion binding phosphate ion binding guanosine phosphorylase activity pentosyltransferase activity glycosyltransferase activity purine-nucleoside phosphorylase activity transferase activity catalytic activity nucleobase binding purine nucleobase binding identical protein binding protein binding	response to stimulus response to chemical response to xenobiotic stimulus deoxyadenosine catabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process deoxyadenosine metabolic process purine deoxyribonucleoside catabolic process nucleobase-containing compound metabolic process 2'-deoxyribonucleoside metabolic process nucleobase-containing small molecule metabolic process purine deoxyribonucleoside metabolic process small molecule metabolic process response to stimulus response to chemical response to xenobiotic stimulus deoxyadenosine catabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process deoxyadenosine metabolic process purine deoxyribonucleoside catabolic process nucleobase-containing compound metabolic process 2'-deoxyribonucleoside metabolic process nucleobase-containing small molecule metabolic process purine deoxyribonucleoside metabolic process small molecule metabolic process carbohydrate derivative catabolic process 2'-deoxyribonucleoside catabolic 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 small molecule catabolic process nucleoside catabolic process metabolic process cellular process small molecule catabolic process purine nucleoside metabolic process immune response immune system process urate biosynthetic process biosynthetic process small molecule biosynthetic process purine-containing compound biosynthetic process urate metabolic process purine deoxyribonucleoside monophosphate catabolic process deoxyribonucleoside monophosphate catabolic process dAMP catabolic process organophosphate catabolic process dAMP metabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process purine nucleoside monophosphate catabolic process purine nucleotide metabolic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process nucleoside monophosphate metabolic process nucleotide catabolic process nucleoside phosphate metabolic process purine nucleotide catabolic process purine deoxyribonucleotide catabolic process nucleoside monophosphate catabolic process 2'-deoxyribonucleotide metabolic process purine deoxyribonucleoside monophosphate metabolic process nucleotide metabolic process organophosphate metabolic process purine deoxyribonucleotide metabolic process nucleotide biosynthetic process nucleobase-containing compound biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic compound salvage purine-containing compound salvage deoxyinosine catabolic process deoxyinosine metabolic process IMP metabolic process ribose phosphate metabolic process ribonucleotide catabolic process purine ribonucleoside monophosphate catabolic process purine ribonucleoside monophosphate metabolic process ribonucleotide metabolic process ribonucleoside monophosphate catabolic process purine ribonucleotide catabolic process IMP catabolic process purine ribonucleotide metabolic process nucleoside biosynthetic process purine ribonucleoside metabolic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process nucleoside salvage purine ribonucleoside biosynthetic process ribonucleoside biosynthetic process nucleobase-containing small molecule biosynthetic process purine ribonucleoside salvage purine nucleoside biosynthetic process ribonucleoside metabolic process multicellular organismal process regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of interleukin-2 production regulation of biological process biological regulation interleukin-2 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of interleukin-2 production regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process nicotinamide riboside catabolic process nicotinamide riboside metabolic process pyridine nucleoside catabolic process pyridine-containing compound metabolic process pyridine nucleoside metabolic process pyridine-containing compound catabolic process allantoin metabolic process inosine catabolic process inosine metabolic process ribonucleoside catabolic process purine ribonucleoside catabolic process positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of leukocyte differentiation regulation of alpha-beta T cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development cell differentiation anatomical structure development alpha-beta T cell activation T cell differentiation developmental process positive regulation of cell development positive regulation of alpha-beta T cell activation leukocyte differentiation positive regulation of alpha-beta T cell differentiation cellular developmental process regulation of developmental process cell development regulation of alpha-beta T cell differentiation regulation of T cell differentiation alpha-beta T cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR011268	Purine nucleoside phosphorylase	Family
A, B, C, D, E A, B, C, D, E, F	IPR018099	Purine phosphorylase, family 2, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR011270	Purine nucleoside phosphorylase I, inosine/guanosine-specific	Family
A, B, C, D, E A, B, C, D, E, F	IPR000845	Nucleoside phosphorylase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P00491	purine nucleoside phosphorylase deficiency osteoporosis Arsenic Poisoning malignant pancreatic neoplasm pancreatic ductal adenocarcinoma ulcerative colitis breast cancer invasive ductal breast carcinoma mature T-cell and NK-cell non-Hodgkin lymphoma osteosarcoma Takayasu arteritis atopic eczema breast carcinoma cutaneous lupus erythematosus drug-induced liver injury purine nucleoside phosphorylase deficiency osteoporosis Arsenic Poisoning malignant pancreatic neoplasm pancreatic ductal adenocarcinoma ulcerative colitis breast cancer invasive ductal breast carcinoma mature T-cell and NK-cell non-Hodgkin lymphoma osteosarcoma Takayasu arteritis atopic eczema breast carcinoma cutaneous lupus erythematosus drug-induced liver injury lung carcinoma medulloblastoma ovarian cancer psoriasis tuberculosis B-cell chronic lymphocytic leukemia ductal breast carcinoma in situ interstitial cystitis

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.