› 2ydx

X-ray diffraction
2.8Å resolution

Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit

Released:
DOI: 10.2210/pdb2ydx/pdb
PDB entry 2ydx coloured by chain, front view.
PDB entry 2ydx coloured by chain, side view.
PDB entry 2ydx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits.
Shafqat N, Muniz JR, Pilka ES, Papagrigoriou E, von Delft F, Oppermann U, Yue WW
Biochem J 452 27-36 (2013)
PMID: 23425511

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192764 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methionine adenosyltransferase 2 subunit beta Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 315 amino acids
Theoretical weight: 35.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NZL9 (Residues: 28-334; Coverage: 92%)
Gene names: MAT2B, MSTP045, Nbla02999, TGR, UNQ2435/PRO4995
Sequence domains: RmlD substrate binding domain
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

5 bound ligands:
Ligand STL 10 x STL
Ligand NAP 4 x NAP
Ligand SO4 19 x SO4
Ligand CA 1 x CA
Ligand TXP 1 x TXP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P42212
Unit cell:
a: 163.389Å b: 163.389Å c: 252.882Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.168 0.188
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification.
Fang et al. (2015)
2 more

8 mentions without citation

Polypharmacology or Promiscuity? Structural Interactions of Resveratrol With Its Bandwagon of Targets.
Saqib et al. (2018)
7 more