› 6qvl

X-ray diffraction
2.28Å resolution

Human SHMT2 in complex with pemetrexed

Released:
DOI: 10.2210/pdb6qvl/pdb
PDB entry 6qvl coloured by chain, front view.
PDB entry 6qvl coloured by chain, side view.
PDB entry 6qvl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs.
Scaletti E, Jemth AS, Helleday T, Stenmark P
FEBS Lett 593 1863-1873 (2019)
PMID: 31127856

Function and Biology Details

Reaction catalysed: 
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152739 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine hydroxymethyltransferase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 504 amino acids
Theoretical weight: 56.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P34897 (Residues: 1-504; Coverage: 100%)
Gene name: SHMT2
Sequence domains: Serine hydroxymethyltransferase

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
4 bound ligands:
Ligand GOL 3 x GOL
Ligand PEG 1 x PEG
Ligand CA 1 x CA
Ligand 4DW 1 x 4DW
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P6522
Unit cell:
a: 160.208Å b: 160.208Å c: 209.442Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.214 0.212 0.259
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Therapeutic Targeting of Mitochondrial One-Carbon Metabolism in Cancer.
Dekhne et al. (2020)
11 more

4 mentions without citation

A Review of Small-Molecule Inhibitors of One-Carbon Enzymes: SHMT2 and MTHFD2 in the Spotlight.
Cuthbertson et al. (2021)
3 more