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Ligand · KDB

KDB · 3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid

KDB, 3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid (C8 H12 O6, 204.2 g/mol), in the MolNFT structures on GenesisL1: bound in 4 records (2 PDB entries). Every binding site with its residues within 4.5 Å, the residues it…

Component
KDB
Formula
C8 H12 O6
Class
sugar
Structures
4
PDB entries
2

Binding sites

KDB in 4 structures; the first of them:

  • 2R1W · Crystal structure of S25-2 Fab in complex with Kdo analogues · KDB C2 · binds ASN30A, ARG30C
  • 3BPC · co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3-dehydro Kdo (4.8) Kdo · KDB C2 · binds ASN30A, ARG30C, TYR32
  • 2R1W · Crystal structure of S25-2 Fab in complex with kdo analogues · KDB C2 · binds ASN30A, ARG30C
  • 3BPC · Co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3- dehydro kdo (4.8) kdo · KDB C2 · binds ASN30A, ARG30C, TYR32

Residues it binds most

ARG 4, ASN 4, TYR 2 (residue and the binding sites it lines).

Found with

  • MG · Magnesium ion
  • ZN · Zinc ion
  • KDA · prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid

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