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Phospho-glucan bound structure of starch phosphatase starch EXCESS4 reveals the mechanism for C6-specificty

Analyse Phospho-glucan bound structure of starch phosphatase starch EXCESS4 reveals the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4PYH
Type
protein
Length
293 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Phosphoglucan phosphatase DSP4, chloroplastic
EC
3.1.3.-
UniProt
Q9FEB5
Ligands
GLC, MG, PO4
Pockets
2 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APhosphoglucan phosphatase DSP4, chloroplastic (EC 3.1.3.-)protein29337% helix, 26% strandQ9FEB5

Ligands and binding sites

  • GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A
  • MG · Magnesium ion · metal · chains A
  • PO4 · Phosphate ion · ion · chains A
  • GOL · Glycerol · additive · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16940.710.7850GLC, PO4
2890.360.7517empty

Compared structures

  • 4PYH · Phospho-glucan bound structure of starch phosphatase Starch EXcess4 reveals the mechanism… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9FEB5 · AlphaFold monomer V2.0 prediction for phosphoglucan phosphatase DSP4, chloroplastic… · a predicted model of the same protein · chain A against A, TM-score 0.99

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