› 8t4o

X-ray diffraction
2.68Å resolution

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF347 inhibitor with no glutamate

Released:
DOI: 10.2210/pdb8t4o/pdb
PDB entry 8t4o coloured by chain, front view.
PDB entry 8t4o coloured by chain, side view.
PDB entry 8t4o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Characterization of 5-Substituted Pyrrolo[3,2-d]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Katinas JM, Nayeen MJ, Schneider M, Shah K, Fifer AN, Klapper LM, Sharma A, Thalluri K, Van Nieuwenhze MS, Hou Z, Gangjee A, Matherly LH, Dann CE
Biochemistry (2024)
PMID: 38324671

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152742 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine hydroxymethyltransferase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 493 amino acids
Theoretical weight: 54.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P34897 (Residues: 29-504; Coverage: 94%)
Gene name: SHMT2
Sequence domains: Serine hydroxymethyltransferase

Ligands and Environments

2 bound ligands:
Ligand Y5C 1 x Y5C
Ligand PLG 2 x PLG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P6522
Unit cell:
a: 158.538Å b: 158.538Å c: 208.009Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.214 0.259
Expression system: Escherichia coli BL21(DE3)

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