Structure of PDB 6dyv Chain A

Receptor sequence

>6dyvA (length=232) Species: 210 (Helicobacter pylori)

QGVQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVA
YSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLV
QHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIA
SGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISD
NADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL

3D structure

• PDB: 6dyv Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
• Chain: A
• Resolution: 1.62 Å

Enzymatic activity

• Enzyme Commision number: 3.2.2.30: aminodeoxyfutalosine nucleosidase.
  3.2.2.9: adenosylhomocysteine nucleosidase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	OS3	A	M10 I52 V78 A79 G80 F153 V154 E173 M174 E175 D198 F208	M12 I54 V80 A81 G82 F155 V156 E175 M176 E177 D200 F210	MOAD: Kd=0.026nM PDBbind-CN: -logKd/Ki=10.59,Kd=0.026nM

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008782 adenosylhomocysteine nucleosidase activity
• GO:0008930 methylthioadenosine nucleosidase activity
• GO:0016787 hydrolase activity
• GO:0102246 6-amino-6-deoxyfutalosine hydrolase activity

Biological Process

• GO:0009086 methionine biosynthetic process
• GO:0009116 nucleoside metabolic process
• GO:0009164 nucleoside catabolic process
• GO:0009234 menaquinone biosynthetic process
• GO:0019284 L-methionine salvage from S-adenosylmethionine
• GO:0019509 L-methionine salvage from methylthioadenosine

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:6dyv, PDBe:6dyv, PDBj:6dyv
• PDBsum: 6dyv
• PubMed: 30860833
• UniProt: Q9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)