Crystal structure at 2.4 ångström resolution of E. COLI serine hydroxymethyltransferase in complex with glycine and 5-formyl tetrahydrofolate

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).

Ligands and binding sites

• PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 4 copies · chains A, B, C, D
• FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 4 copies · chains A, B, D, C

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 4637 Ų buried · 57 hydrogen bonds · protein-protein
• C–D · 4561 Ų buried · 57 hydrogen bonds · protein-protein
• A–D · 351 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 342 Ų buried · 2 hydrogen bonds · protein-protein
• B–D · 64 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 1DFO · Crystal structure at 2.4 ångström resolution of E. COLI serine hydroxymethyltransferase… · the same entry in another collection · chain D against D, TM-score 1.00
• P0A825 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (P0A825) · a predicted model of the same protein · chain D 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 P0A825
• Elsewhere: RCSB PDB 1DFO · PDBe 1DFO · UniProt P0A825