4WKP | pdb_00004wkp

Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with 2-(2-hydroxyethoxy)ethylthiomethyl-DADMe-Immucillin-A

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d4wkpd1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Helicobacter pylori J99 ) [TaxId: 85963 ],	SCOPe (2.08)
D	d4wkpd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Helicobacter pylori J99 ) [TaxId: 85963 ],	SCOPe (2.08)
C	d4wkpc1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Helicobacter pylori J99 ) [TaxId: 85963 ],	SCOPe (2.08)
C	d4wkpc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Helicobacter pylori J99 ) [TaxId: 85963 ],	SCOPe (2.08)
B	d4wkpb1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Helicobacter pylori J99 ) [TaxId: 85963 ],	SCOPe (2.08)
B	d4wkpb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Helicobacter pylori J99 ) [TaxId: 85963 ],	SCOPe (2.08)
A	d4wkpa1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Helicobacter pylori J99 ) [TaxId: 85963 ],	SCOPe (2.08)
A	d4wkpa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Helicobacter pylori J99 ) [TaxId: 85963 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Purine and uridine phosphorylases	8100770	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8100770	3000626	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8100770	3000626	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8100770	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)
D		e4wkpD1	A: alpha bundles	X: CBS-domain	H: Porins	T: Invertebrate chitin-binding proteins	F:	ECOD (develop294)
C		e4wkpC1	A: alpha bundles	X: CBS-domain	H: Porins	T: Invertebrate chitin-binding proteins	F:	ECOD (develop294)
B		e4wkpB1	A: alpha bundles	X: CBS-domain	H: Porins	T: Invertebrate chitin-binding proteins	F:	ECOD (develop294)
A		e4wkpA1	A: alpha bundles	X: CBS-domain	H: Porins	T: Invertebrate chitin-binding proteins	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Aminodeoxyfutalosine nucleosidase	hydrolase activity, acting on glycosyl bonds purine nucleosidase activity hydrolase activity methylthioadenosine nucleosidase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity 6-amino-6-deoxyfutalosine hydrolase activity adenosylhomocysteine nucleosidase activity	oxoacid metabolic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process oxoacid metabolic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process metabolic compound salvage small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic 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 biosynthetic process L-methionine salvage from methylthioadenosine proteinogenic amino acid biosynthetic process metabolic process cellular process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process ketone metabolic process menaquinone metabolic process menaquinone biosynthetic process ketone biosynthetic process carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process glycosyl compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule catabolic process nucleobase-containing small molecule metabolic process nucleoside catabolic process small molecule catabolic process S-adenosylmethionine metabolic process S-adenosylmethionine cycle L-methionine salvage from S-adenosylmethionine	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C, D	IPR000845	Nucleoside phosphorylase domain	Domain
A, B, C, D	IPR010049	MTA/SAH nucleosidase	Family

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.