6DZ3

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-butyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol

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)
A	d6dz3a_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	5'-deoxy-5'-methylthioadenosine phosphorylase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6dz3b_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	5'-deoxy-5'-methylthioadenosine phosphorylase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6dz3c_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	5'-deoxy-5'-methylthioadenosine phosphorylase	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)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8036168	3000626	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8036168	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8036168	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	e6dz3A1	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	e6dz3B1	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	e6dz3C1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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	S-methyl-5'-thioadenosine phosphorylase	1,4-alpha-oligoglucan phosphorylase activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity pentosyltransferase activity S-methyl-5-thioadenosine phosphorylase activity purine-nucleoside phosphorylase activity	nucleobase-containing compound metabolic process primary metabolic process metabolic process glycosyl compound metabolic process carbohydrate derivative metabolic process nucleoside biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process small molecule metabolic process cellular metabolic compound salvage purine ribonucleoside metabolic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process purine-containing compound salvage nucleobase-containing compound metabolic process primary metabolic process metabolic process glycosyl compound metabolic process carbohydrate derivative metabolic process nucleoside biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process small molecule metabolic process cellular metabolic compound salvage purine ribonucleoside metabolic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process purine-containing compound salvage small molecule biosynthetic process nucleoside salvage cellular metabolic process purine ribonucleoside biosynthetic process ribonucleoside biosynthetic process nucleobase-containing compound biosynthetic process nucleoside metabolic process nucleobase-containing small molecule biosynthetic process purine-containing compound metabolic process purine ribonucleoside salvage biosynthetic process purine nucleoside biosynthetic process cellular process purine nucleoside metabolic process ribonucleoside metabolic process response to ketone response to lipid response to stimulus response to chemical response to oxygen-containing compound response to testosterone response to organic cyclic compound methylation oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process sulfur compound metabolic process L-methionine biosynthetic process methionine biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process L-methionine salvage from methylthioadenosine proteinogenic amino acid biosynthetic process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C	IPR018099	Purine phosphorylase, family 2, conserved site	Conserved Site
A, B, C	IPR010044	Methylthioadenosine phosphorylase (MTAP)	Family
A, B, C	IPR000845	Nucleoside phosphorylase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q13126	melanoma diaphyseal medullary stenosis-bone malignancy syndrome prostate cancer cutaneous melanoma non-small cell lung carcinoma ovarian carcinoma psoriasis acute lymphoblastic leukemia skin neoplasm brain glioma Diaphyseal medullary stenosis with bone malignancy glioblastoma large cell medulloblastoma malignant mesothelioma open-angle glaucoma melanoma diaphyseal medullary stenosis-bone malignancy syndrome prostate cancer cutaneous melanoma non-small cell lung carcinoma ovarian carcinoma psoriasis acute lymphoblastic leukemia skin neoplasm brain glioma Diaphyseal medullary stenosis with bone malignancy glioblastoma large cell medulloblastoma malignant mesothelioma open-angle glaucoma plasma cell myeloma prostate carcinoma sarcoma adrenal cortex carcinoma breast carcinoma heart disease lung adenocarcinoma medulloblastoma ovarian cancer primitive neuroectodermal tumor skin basal cell carcinoma B-cell acute lymphoblastic leukemia inflammatory bowel disease lung carcinoma melanocytic nevus

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.