A. thaliana serine hydroxymethyltransferase isoform 2 (ATSHMT2) in complex with pemetrexed

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).

Ligands and binding sites

• PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · 3 copies · chains A, B, C, D
• LYA · 2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)-ethyl]-benzoylamino}-pentanedioic acid · ligand · 3 copies · chains A, B, C, D
• SER · Serine · ligand · chains C, D
• PLP · Pyridoxal-5'-phosphate · ligand · chains C, D
• EDO · 1,2-ethanediol · additive · 38 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 5043 Ų buried · 58 hydrogen bonds · protein-protein
• C–D · 4976 Ų buried · 59 hydrogen bonds · protein-protein
• A–D · 851 Ų buried · 15 hydrogen bonds · protein-protein
• B–C · 756 Ų buried · 14 hydrogen bonds · protein-protein
• A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).

Compared structures

• 6SMW · A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with pemetrexed · the same entry in another collection · chain A against A, TM-score 1.00
• Q94C74 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase 2, mitochondrial… · a predicted model of the same protein · chain C against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q94C74
• Elsewhere: RCSB PDB 6SMW · PDBe 6SMW · UniProt Q94C74