Crystal structure of arabidopsis thaliana PDX1-I320-G3P complex

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).

Ligands and binding sites

• K8P · [(2~{R},3~{R})-2,3-bis(oxidanyl)-3-[[(2~{S})-3-oxidanylidenepent-4-en-2-yl]amino]propyl] dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
• RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · 4 copies · chains A, D, B, C
• HG3 · [(2~{R})-2,3,3-tris(oxidanyl)propyl] dihydrogen phosphate · ligand · 4 copies · chains A, D, B, C
• GOL · Glycerol · additive · 2 copies · chains A, C, D, B

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 1018 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 995 Ų buried · 12 hydrogen bonds · protein-protein
• B–C · 994 Ų buried · 9 hydrogen bonds · protein-protein
• A–D · 991 Ų buried · 9 hydrogen bonds · protein-protein
• A–C · 452 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

• 5LNW · Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex · the same entry in another collection · chain D against D, TM-score 1.00
• Q8L940 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit PDX1.3… · 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 Q8L940
• Elsewhere: RCSB PDB 5LNW · PDBe 5LNW · UniProt Q8L940