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Ligand · PDD

PDD · N-(5'-phosphopyridoxyl)-D-alanine

PDD, N-(5'-phosphopyridoxyl)-D-alanine (C11 H17 N2 O7 P, 320.2 g/mol), in the MolNFT structures on GenesisL1: bound in 10 records (5 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the…

Component
PDD
Formula
C11 H17 N2 O7 P
Class
ligand
Structures
10
PDB entries
5

Binding sites

PDD in 10 structures; the first of them:

  • 1L6G · Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine · PDD A390 · binds VAL37, LYS39, TYR43, LEU85, KCX129, ARG136, TYR164, HIS166 and 11 more
  • 2BMK · Fab fragment of PLP-dependent catalytic antibody 15A9 in complex with… · PDD B1217 · binds ASN31, TYR32, HIS34, ARG91, SER92, TYR94, PHE96, TYR33 and 6 more
  • 2ZPU · Crystal Structure of Modified Serine Racemase from S.pombe. · PDD A350 · binds PHE56, LYS57, PHE80, SER81, SER82, GLY83, ASN84, HIS85 and 15 more
  • 2ZR8 · Crystal Structure of Modified Serine Racemase complexed with Serine · PDD A350 · binds PHE56, LYS57, PHE80, SER81, SER82, GLY83, ASN84, HIS85 and 15 more
  • 3DAA · Crystallographic structure of D-amino acid aminotransferase inactivated by… · PDD A285 · binds TYR31, VAL33, HIS47, ARG50, ARG138, LYS145, GLU177, GLY178 and 15 more
  • 1L6G · Alanine racemase bound with N-(5'-phosphopyridoxyl)-D- alanine · PDD A390 · binds VAL37, LYS39, TYR43, LEU85, KCX129, ARG136, TYR164, HIS166 and 11 more
  • 2BMK · Fab fragment of plp-dependent catalytic antibody 15A9 in complex with… · PDD B1217 · binds ASN31, TYR32, HIS34, ARG91, SER92, TYR94, PHE96, TYR33 and 6 more
  • 2ZPU · Crystal structure of modified serine racemase from S.POMBE. · PDD A350 · binds PHE56, LYS57, PHE80, SER81, SER82, GLY83, ASN84, HIS85 and 15 more
  • 2ZR8 · Crystal structure of modified serine racemase complexed with serine · PDD A350 · binds PHE56, LYS57, PHE80, SER81, SER82, GLY83, ASN84, HIS85 and 15 more
  • 3DAA · Crystallographic structure of D-amino acid aminotransferase inactivated by… · PDD A285 · binds TYR31, VAL33, HIS47, ARG50, ARG138, LYS145, GLU177, GLY178 and 15 more

Residues it binds most

GLY 12, TYR 16, SER 16, ARG 12, HIS 16, PHE 12, THR 8, LEU 14, LYS 16, ASN 14 (residue and the binding sites it lines).

Found with

  • MG · Magnesium ion
  • SER · Serine
  • IOD · Iodide ion

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