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Ligand · XYZ

XYZ · Beta-D-xylofuranose

XYZ, Beta-D-xylofuranose (C5 H10 O5, 150.1 g/mol), in the MolNFT structures on GenesisL1: bound in 4 records (4 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands found with it.

Component
XYZ
Formula
C5 H10 O5
Class
ligand
Structures
4
PDB entries
4

Binding sites

XYZ in 4 structures; the first of them:

  • 5XIS · Crystal structure of RNF168 UDM1 in complex with LYS63-linked diubiquitin, form I · XYZ A201 · binds SER134, GLU138, TYR59, ASN60
  • 7EY1 · Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl with intermediate substrate xylose · XYZ B909 · binds ASP109, LEU158, ARG174, LYS207, HIS208, MET265, TYR268, ASP300 and 3 more
  • 7EY2 · Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl D300N mutant with intermediate substrate xylose · XYZ A907 · binds ASP109, LEU158, ARG174, LYS207, HIS208, MET265, TYR268, ASN300 and 3 more
  • 7F95 · Bifunctional XYLOSIDASE/GLUCOSIDASE lxyl with intermediate substrate xylose for 2 min · XYZ B906 · binds ASP109, ARG174, LYS207, HIS208, MET265, TYR268, ASP300, TRP301 and 2 more

Residues it binds most

GLU 6, ASP 4, ARG 5, SER 5, TYR 5, HIS 4, LYS 4, MET 4, TRP 4, ASN 3 (residue and the binding sites it lines).

Found with

  • BMA · beta-D-mannopyranose
  • MAN · alpha-D-mannopyranose
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose
  • BKR · Deacetyltaxol
  • XYL · Xylitol
  • MG · Magnesium ion
  • XYP · beta-D-xylopyranose

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