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Ligand · GCD

GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid

GCD, 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid (C6 H8 O6, 176.1 g/mol), in the MolNFT structures on GenesisL1: bound in 28 records (18 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and…

Component
GCD
Formula
C6 H8 O6
Class
sugar
Structures
28
PDB entries
18

Binding sites

GCD in 28 structures; the first of them:

  • 5GUB · Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated… · GCD D2 · binds TYR146, ARG204, TRP284, ALA286, SER287, ARG322, LEU389, ARG393 and 5 more
  • 5GX6 · Crystal structure of solute-binding protein complexed with unsaturated chondroitin… · GCD D2 · binds TYR146, TRP284, ALA286, SER287, ARG322, LEU389, ARG393, GLN405 and 3 more
  • 5GX7 · Crystal structure of solute-binding protein complexed with unsaturated chondroitin… · GCD D2 · binds TYR146, ARG204, TRP284, ALA286, SER287, ARG322, LEU389, ARG393 and 4 more
  • 5UAS · Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase bound to… · GCD C4 · binds ASN60, THR355
  • 5XS8 · Crystal structure of solute-binding protein complexed with unsaturated chondroitin… · GCD E2 · binds TYR146, ARG204, TRP284, ALA286, SER287, ARG322, LEU389, ARG393 and 5 more
  • 6BYT · Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate · GCD C4 · binds PHE80, GLY81, THR387
  • 6BYX · Complex structure of LOR107 mutant (R259N) with tetrasaccharide substrate · GCD C4 · binds TYR330, HIS384, VAL386, ARG406
  • 6INZ · Crystal structure of solute-binding protein complexed with unsaturated hyaluronan… · GCD B2 · binds TYR146, TRP284, ALA286, SER287, ARG322, LEU389, GLN405, TYR409 and 2 more
  • 6LJL · Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate · GCD B4 · binds ALA389, HIS392, VAL393, SER442, GLN446, ARG757
  • 6X3M · Crystal structure of full-length Streptococcal bacteriophage hyaluronidase in complex… · GCD J4 · binds LEU255, LYS259
  • 7EIQ · Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 4S · GCD B2 · binds ASP444, ARG500, HIS501, TYR508, ARG560, TYR655

Residues it binds most

ARG 38, TYR 31, TRP 22, LEU 32, GLN 21, ALA 26, SER 23, ASN 19, LYS 23, HIS 22 (residue and the binding sites it lines).

Found with

  • CA · Calcium ion
  • BDP · beta-D-glucopyranuronic acid
  • MG · Magnesium ion
  • 83Y · 3-O-sulfo-alpha-L-rhamnopyranose
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose
  • SO4 · Sulfate ion
  • GOL · Glycerol
  • EDO · 1,2-ethanediol
  • ASG · 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose
  • 8EX · 2-acetamido-2-deoxy-4,6-di-O-sulfo-beta-D-galactopyranose
  • NG6 · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose
  • NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose

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