1W79 Hydrolase date Aug 31, 2004
title Crystal Structure Of The Dd-Transpeptidase-Carboxypeptidase Actinomadura R39
authors E.Sauvage, R.Herman, S.Petrella, C.Duez, J.M.Frere, P.Charlier
compound source
Molecule: D-Alanyl-D-Alanine Carboxypeptidase
Chain: A, B, C, D
Synonym: Dd-Peptidase,Penicillin-Binding Protein,Pbp
Ec: 3.4.16.4
Engineered: Yes
 Organism_scientific: Actinomadura Sp. R39
Organism_taxid: 72570
Gene: Dac
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.214 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.187 93.369 107.272 90.00 94.25 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand MG, SO4 enzyme Hydrolase E.C.3.4.16.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins., Sauvage E, Herman R, Petrella S, Duez C, Bouillenne F, Frere JM, Charlier P, J Biol Chem. 2005 Sep 2;280(35):31249-56. Epub 2005 Jun 29. PMID:15987687
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (312 Kb) [Save to disk]
  • Biological Unit Coordinates (1w79.pdb1.gz) 81 Kb
  • Biological Unit Coordinates (1w79.pdb2.gz) 81 Kb
  • Biological Unit Coordinates (1w79.pdb3.gz) 81 Kb
  • Biological Unit Coordinates (1w79.pdb4.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 1W79
  • CSU: Contacts of Structural Units for 1W79
  • Likely Quarternary Molecular Structure file(s) for 1W79
  • Structure Factors (1634 Kb)
  • Retrieve 1W79 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1W79 from S2C, [Save to disk]
  • Re-refined 1w79 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1W79 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 1W79
  • 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 1W79, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1w79_C] [1w79_A] [1w79] [1w79_B] [1w79_D]
  • SWISS-PROT database: [P39045]
  • Domain organization of [DAC_ACTSP] by SWISSPFAM
    • Other resources with information on 1W79
  • Community annotation for 1W79 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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