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Crystal structure of B. subtilis 168 glpq in complex with glycerol-3- phosphate (5 minute soak)

Analyse Crystal structure of B. subtilis 168 glpq in complex with glycerol-3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5T9B
Type
protein
Length
259 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Glycerophosphoryl diester phosphodiesterase
EC
3.1.4.46
UniProt
P37965
Ligands
G3P, CA, NA
Pockets
1 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
GGlycerophosphoryl diester phosphodiesterase (EC 3.1.4.46)protein25940% helix, 17% strandP37965

Ligands and binding sites

  • G3P · Sn-glycerol-3-phosphate · ligand · chains G
  • CA · Calcium ion · metal · chains G
  • NA · Sodium ion · metal · chains G

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1700.390.7922CA, G3P

Compared structures

  • 5T9B · Crystal structure of B. subtilis 168 GlpQ in complex with glycerol-3-phosphate (5 minute… · the same entry in another collection · chain G against G, TM-score 1.00
  • P37965 · AlphaFold monomer V2.0 prediction for glycerophosphodiester phosphodiesterase (P37965) · a predicted model of the same protein · chain G against A, TM-score 0.99

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