6T1B | pdb_00006t1b

Crystal structure of YlmD from Geobacillus stearothermophilus in complex with inosine

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)
A	d6t1ba_	Alpha and beta proteins (a+b)	CNF1/YfiH-like putative cysteine hydrolases	CNF1/YfiH-like putative cysteine hydrolases	YfiH-like	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CNF1/YfiH-like putative cysteine hydrolases	8040083	3001230	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	JmjC,JmjN	e6t1bA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: JmjC,JmjN	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.140.10	Alpha Beta	4-Layer Sandwich	CNF1/YfiH-like putative cysteine hydrolases	CNF1/YfiH-like putative cysteine hydrolases	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	YlmD	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines adenosine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds pentosyltransferase activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines adenosine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds pentosyltransferase activity glycosyltransferase activity purine-nucleoside phosphorylase activity transferase activity S-methyl-5-thioadenosine phosphorylase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011324	Cytotoxic necrotizing factor-like, catalytic	Homologous Superfamily
A	IPR003730	Multi-copper polyphenol oxidoreductase	Family
A	IPR038371	Multi-copper polyphenol oxidoreductase superfamily	Homologous Superfamily

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.