2XDM Hydrolase Inhibitor date May 04, 2010
title Crystal Structure Of A Complex Between Actinomadura R39 Dd P And A Peptidoglycan Mimetic Boronate Inhibitor
authors M.Rocaboy, E.Sauvage, R.Herman, F.Kerff, P.Charlier
compound source
Molecule: D-Alanyl-D-Alanine Carboxypeptidase
Chain: A, B, C, D
Synonym: Dd-Peptidase, Dd-Carboxypeptidase, Penicillin-Bind Protein, Pbp;
Ec: 3.4.16.4
 Organism_scientific: Actinomadura
Organism_taxid: 72570
Strain: R39
symmetry Space Group: P 1 21 1
R_factor 0.199 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.308 91.568 106.871 90.00 94.37 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand BO8, CO, MES, SO4 enzyme Hydrolase E.C.3.4.16.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal Structure of a Complex between the Actinomadura R39 dd-Peptidase and a Peptidoglycan-mimetic Boronate Inhibitor: Interpretation of a Transition State Analogue in Terms of Catalytic Mechanism., Dzhekieva L, Rocaboy M, Kerff F, Charlier P, Sauvage E, Pratt RF, Biochemistry. 2010 Jul 7. PMID:20608745
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (562 Kb) [Save to disk]
  • Biological Unit Coordinates (2xdm.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (2xdm.pdb2.gz) 141 Kb
  • Biological Unit Coordinates (2xdm.pdb3.gz) 142 Kb
  • Biological Unit Coordinates (2xdm.pdb4.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 2XDM
  • CSU: Contacts of Structural Units for 2XDM
  • Structure Factors (1331 Kb)
  • Retrieve 2XDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XDM from S2C, [Save to disk]
  • Re-refined 2xdm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2XDM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 2XDM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2XDM, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xdm_C] [2xdm_D] [2xdm_A] [2xdm] [2xdm_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2XDM
  • Community annotation for 2XDM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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