› 5xmv

X-ray diffraction
2.16Å resolution

Plasmodium vivax SHMT bound with PLP-glycine and GS362

Released:
DOI: 10.2210/pdb5xmv/pdb
Model geometry
Fit model/data
PDB entry 5xmv coloured by chain, front view.
PDB entry 5xmv coloured by chain, side view.
PDB entry 5xmv coloured by chain, top view.
Source organism: Plasmodium vivax
Primary publication:
Conformational Aspects in the Design of Inhibitors for Serine Hydroxymethyltransferase (SHMT): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs.
Schwertz G, Frei MS, Witschel MC, Rottmann M, Leartsakulpanich U, Chitnumsub P, Jaruwat A, Ittarat W, Schäfer A, Aponte RA, Trapp N, Mark K, Chaiyen P, Diederich F
Chemistry 23 14345-14357 (2017)
PMID: 28967982

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-107691 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
glycine hydroxymethyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 442 amino acids
Theoretical weight: 49.25 KDa
Source organism: Plasmodium vivax
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A5K8L9 (Residues: 1-442; Coverage: 100%)
Gene name: PVX_100730
Sequence domains: Serine hydroxymethyltransferase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand PLG 3 x PLG
Ligand 8AU 3 x 8AU
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: C2
Unit cell:
a: 101.674Å b: 58.843Å c: 234.899Å
α: 90° β: 90.14° γ: 90°
R-values:
R R work R free
0.248 0.242 0.306
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Targeting cancer metabolism in the era of precision oncology.
Stine et al. (2022)
1 more