2I87 Ligase date Sep 01, 2006
title Allosteric Inhibition Of Staphylococcus Aureus D-Alanine:D-A Ligase Revealed By Crystallographic Studies
authors S.Liu, J.S.Chang, J.T.Herberg, M.Horng, P.K.Tomich, A.H.Lin, K.R.M
compound source
Molecule: D-Alanine-D-Alanine Ligase
Chain: A, B
Synonym: D-Alanylalanine Synthetase, D-Ala-D-Ala Ligase
Ec: 6.3.2.4
Engineered: Yes
Organism_scientific: Staphylococcus Aureus Subsp. Aureus
Organism_taxid: 93062
Strain: Col
Gene: Ddl
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: M15[Prep4]
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe-60
symmetry Space Group: P 1 21 1
R_factor 0.200 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.661 66.408 78.590 90.00 96.24 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand SO4 enzyme Ligase E.C.6.3.2.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAllosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies., Liu S, Chang JS, Herberg JT, Horng MM, Tomich PK, Lin AH, Marotti KR, Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15178-83. Epub 2006 Oct 2. PMID:17015835
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (2i87.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 2I87
  • CSU: Contacts of Structural Units for 2I87
  • Likely Quarternary Molecular Structure file(s) for 2I87
  • Structure Factors (412 Kb)
  • Retrieve 2I87 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2I87 from S2C, [Save to disk]
  • Re-refined 2i87 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2I87 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 2I87
  • 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 2I87, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2i87_A] [2i87] [2i87_B]
  • SWISS-PROT database: [Q5HEB7]
  • Domain organization of [DDL_STAAC] by SWISSPFAM
  • Other resources with information on 2I87
  • Community annotation for 2I87 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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