6DYU

Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((prop-2-yn-1-ylthio)methyl)pyrrolidin-3-ol

Summary for 6DYU

Descriptor5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase, 1,2-ETHANEDIOL, (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(prop-2-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol, ... (5 entities in total)
Functional Keywordsmtan enzyme, duodenal ulcers, stomach cancer, hydrolase
Biological sourceHelicobacter pylori (Campylobacter pylori)
Total number of polymer chains2
Total molecular weight55003.26
Authors
Harijan, R.K.,Ducati, R.G.,Bonanno, J.B.,Almo, S.C.,Schramm, V.L. (deposition date: 2018-07-02, release date: 2019-03-20, Last modification date: 2019-04-10)
Primary citation
Harijan, R.K.,Hoff, O.,Ducati, R.G.,Firestone, R.S.,Hirsch, B.M.,Evans, G.B.,Schramm, V.L.,Tyler, P.C.
Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
J. Med. Chem., 2019
PubMed: 30860833 (PDB entries with the same primary citation)
DOI: 10.1021/acs.jmedchem.8b01642
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.6 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers 0.20340 1.0% 0.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 6dyu
no rotation
Molmil generated image of 6dyu
rotated about x axis by 90°
Molmil generated image of 6dyu
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 6dyu
no rotation
Molmil generated image of 6dyu
rotated about x axis by 90°
Molmil generated image of 6dyu
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (6dyu.pdb1.gz [85.5 KB])
Coordinate files for Biological unit (6dyu.pdb2.gz [85.86 KB])