› 6dz0

X-ray diffraction
1.62Å resolution

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol

Released:
DOI: 10.2210/pdb6dz0/pdb
PDB entry 6dz0 coloured by chain, front view.
PDB entry 6dz0 coloured by chain, side view.
PDB entry 6dz0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Harijan RK, Hoff O, Ducati RG, Firestone RS, Hirsch BM, Evans GB, Schramm VL, Tyler PC
J Med Chem 62 3286-3296 (2019)
PMID: 30860833

Function and Biology Details

Reaction catalysed: 
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171545 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
S-methyl-5'-thioadenosine phosphorylase Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 33.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13126 (Residues: 1-283; Coverage: 100%)
Gene names: MSAP, MTAP
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

4 bound ligands:
Ligand PO4 1 x PO4
Ligand EDO 5 x EDO
Ligand OS3 1 x OS3
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P321
Unit cell:
a: 121.812Å b: 121.812Å c: 44.372Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.156 0.155 0.176
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Helicobacter pylori treatment in the post-antibiotics era-searching for new drug targets.
Roszczenko-Jasińska et al. (2020)
2 other articles

1 mention without citation

Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Harijan et al. (2019)