Structure of PDB 4ynb Chain A

Receptor sequence

>4ynbA (length=230) Species: 85963 (Helicobacter pylori J99)

VQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYS
KIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQH
DVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASG
DQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNA
DEKAGMSFDEFLEKSAHTSAKFLKSMVDEL

3D structure

• PDB: 4ynb New Antibiotic Candidates against Helicobacter pylori.
• Chain: A
• Resolution: 2.0 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	4EH	A	M11 I53 V79 A80 G81 F154 V155 V173 E174 M175 E176 D199 F209	M10 I52 V78 A79 G80 F153 V154 V172 E173 M174 E175 D198 F208	MOAD: Ki=0.043nM PDBbind-CN: -logKd/Ki=10.37,Ki=0.043nM

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:4ynb, PDBe:4ynb, PDBj:4ynb
• PDBsum: 4ynb
• PubMed: 26494017
• UniProt: Q9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)