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Ligand · KDA

KDA · prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid

KDA, prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid (C11 H18 O8, 278.3 g/mol), in the MolNFT structures on GenesisL1: bound in 36 records (18 PDB entries). Every binding site with its residues within 4.5 Å, the residues…

Component
KDA
Formula
C11 H18 O8
Class
sugar
Structures
36
PDB entries
18

Binding sites

KDA in 36 structures; the first of them:

  • 2R1W · Crystal structure of S25-2 Fab in complex with Kdo analogues · KDA C1 · binds ASN30A, TYR32, SER91, TYR92, ASN93, ARG95, TYR33, PHE50 and 4 more
  • 2R1X · Crystal structure of S25-2 Fab in complex with Kdo analogues · KDA C1 · binds ASN30A, TYR32, SER91, TYR92, ASN93, ARG95, TYR33, PHE50 and 4 more
  • 2R23 · Crystal structure of S25-2 Fab in complex with Kdo analogues · KDA C1 · binds ARG30C, TYR33, ARG52, ASN52D, HIS96, GLY98
  • 2R2B · Crystal structure of S25-2 Fab in complex with Kdo analogues · KDA C1 · binds ALA52C, ASN52D, GLY52E
  • 3BPC · co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3-dehydro Kdo (4.8) Kdo · KDA C1 · binds ASN30A, TYR32, SER91, TYR92, ASN93, ARG95, TYR33, PHE50 and 4 more
  • 3HZK · Crystal structure of S73-2 antibody in complex with antigen Kdo(2.4)Kdo · KDA C1 · binds ARG27F, TYR32, TYR33, ARG52, LYS53, ILE96, PRO98, TYR100C
  • 3HZV · Crystal structure of S73-2 antibody in complex with antigen Kdo(2.8)Kdo(2.4)Kdo · KDA C1 · binds TYR33, LYS53, ILE96, PRO98
  • 3HZY · Crystal structure of S73-2 antibody in complex with antigen Kdo(2.4)Kdo(2.4)Kdo · KDA C1 · binds ASN27D, ARG27F
  • 3I02 · Crystal structure of S54-10 antibody in complex with antigen Kdo(2.4)Kdo(2.4)Kdo · KDA E1 · binds ASN27D, ARG27F, PHE99
  • 3IJY · Structure of S67-27 in Complex with Kdo(2.8)Kdo · KDA E1 · binds ARG27F, TYR33, LYS53
  • 3OKK · Crystal structure of S25-39 in complex with Kdo(2.4)Kdo · KDA C1 · binds ARG27F, TYR33, ARG52, LYS56, HIS102
  • 3OKL · Crystal structure of S25-39 in complex with Kdo(2.8)Kdo · KDA C1 · binds ARG27F, TYR33, LYS53, HIS96, GLY98
  • 3OKN · Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo · KDA C1 · binds ASN27D, ARG27F
  • 3OKO · Crystal structure of S25-39 in complex with Kdo(2.8)Kdo(2.4)Kdo · KDA C1 · binds ARG27F
  • 3SY0 · S25-2- A(2-8)-A(2-4)KDO trisaccharide complex · KDA C1 · binds ARG30C
  • 3T65 · S25-2- A(2-8)KDO disaccharide complex · KDA C1 · binds TYR33, ASN52D, HIS96, GLY98, TYR99, ARG30C
  • 3T77 · S25-2- A(2-4)KDO disaccharide complex · KDA C1 · binds ARG30C, TYR33, ARG52, ASN52D, HIS96
  • 4M7J · Crystal structure of S25-26 in complex with Kdo(2.8)Kdo(2.4)Kdo trisaccharide · KDA A1 · binds TRP52, SER53, GLY54, GLY55, SER56
  • 2R1W · Crystal structure of S25-2 Fab in complex with kdo analogues · KDA C1 · binds ASN30A, TYR32, SER91, TYR92, ASN93, ARG95, TYR33, PHE50 and 4 more
  • 2R1X · Crystal structure of S25-2 Fab in complex with kdo analogues · KDA C1 · binds ASN30A, TYR32, SER91, TYR92, ASN93, ARG95, TYR33, PHE50 and 4 more
  • 2R23 · Crystal structure of S25-2 Fab in complex with kdo analogues · KDA C1 · binds ARG30C, TYR33, ARG52, ASN52D, HIS96, GLY98
  • 2R2B · Crystal structure of S25-2 Fab in complex with kdo analogues · KDA C1 · binds ALA52C, ASN52D, GLY52E
  • 3BPC · Co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3- dehydro kdo (4.8) kdo · KDA C1 · binds ASN30A, TYR32, SER91, TYR92, ASN93, ARG95, TYR33, PHE50 and 4 more
  • 3HZK · Crystal structure of S73-2 antibody in complex with antigen KDO(2.4) kdo · KDA C1 · binds ARG27F, TYR32, TYR33, ARG52, LYS53, ILE96, PRO98, TYR100C
  • 3HZV · Crystal structure of S73-2 antibody in complex with antigen KDO(2.8) KDO(2.4)KDO · KDA C1 · binds TYR33, LYS53, ILE96, PRO98
  • 3HZY · Crystal structure of S73-2 antibody in complex with antigen KDO(2.4) KDO(2.4)KDO · KDA C1 · binds ASN27D, ARG27F
  • 3I02 · Crystal structure of S54-10 antibody in complex with antigen KDO(2.4) KDO(2.4)KDO · KDA E1 · binds ASN27D, ARG27F, PHE99
  • 3IJY · Structure of S67-27 in complex with KDO(2.8)KDO · KDA E1 · binds ARG27F, TYR33, LYS53
  • 3OKK · Crystal structure of S25-39 in complex with KDO(2.4)KDO · KDA C1 · binds ARG27F, TYR33, ARG52, LYS56, HIS102
  • 3OKL · Crystal structure of S25-39 in complex with KDO(2.8)KDO · KDA C1 · binds ARG27F, TYR33, LYS53, HIS96, GLY98
  • 3OKN · Crystal structure of S25-39 in complex with KDO(2.4)KDO(2.4)KDO · KDA C1 · binds ASN27D, ARG27F
  • 3OKO · Crystal structure of S25-39 in complex with KDO(2.8)KDO(2.4)KDO · KDA C1 · binds ARG27F
  • 3SY0 · S25-2- A(2-8)-A(2-4)KDO trisaccharide complex · KDA C1 · binds ARG30C
  • 3T65 · S25-2- A(2-8)KDO disaccharide complex · KDA C1 · binds TYR33, ASN52D, HIS96, GLY98, TYR99, ARG30C
  • 3T77 · S25-2- A(2-4)KDO disaccharide complex · KDA C1 · binds ARG30C, TYR33, ARG52, ASN52D, HIS96
  • 4M7J · Crystal structure of S25-26 in complex with KDO(2.8)KDO(2.4)KDO trisaccharide · KDA A1 · binds TRP52, SER53, GLY54, GLY55, SER56

Residues it binds most

ARG 34, TYR 24, ASN 22, HIS 16, GLY 10, LYS 12, PHE 10, SER 8, GLU 6, ILE 4 (residue and the binding sites it lines).

Found with

  • ZN · Zinc ion
  • KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
  • MG · Magnesium ion
  • KDB · 3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid
  • K · Potassium ion
  • KDD · 2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid
  • KO1 · D-glycero-alpha-D-talo-oct-2-ulopyranosonic acid
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose
  • PEG · Di(hydroxyethyl)ether

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