2JFF Ligase date Feb 01, 2007
title Crystal Structure Of Murd Ligase In Complex With D-Glu Conta Sulfonamide Inhibitor
authors M.Kotnik, J.Humljan, C.Contreras-Martel, M.Oblak, K.Kristan, M.He D.Blanot, U.Urleb, S.Gobec, A.Dessen, T.Solmajer
compound source
Molecule: Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase
Chain: A
Synonym: Udp-N-Acetylmuramoyl-L-Alanyl-D-Glutamate Ligase, Acetylmuramoyl-L-Alanyl-D-Glutamate Synthetase, D-Glutamic Adding Enzyme;
Ec: 6.3.2.9
Engineered: Yes
Other_details: Inhibitor N-(6-Butoxy-Naphthalene-2-Sulfonyl Glutamic Acid Bound
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli Dh5[Alpha]
Expression_system_taxid: 668369
Expression_system_plasmid: Pabd16
symmetry Space Group: P 41
R_factor 0.173 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.288 65.288 135.060 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.89 Å
ligand KCX, LK2, SO4 BindingDB enzyme Ligase E.C.6.3.2.9 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase., Kotnik M, Humljan J, Contreras-Martel C, Oblak M, Kristan K, Herve M, Blanot D, Urleb U, Gobec S, Dessen A, Solmajer T, J Mol Biol. 2007 Jun 29;370(1):107-15. Epub 2007 May 4. PMID:17507028
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (2jff.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 2JFF
  • CSU: Contacts of Structural Units for 2JFF
  • Likely Quarternary Molecular Structure file(s) for 2JFF
  • Structure Factors (340 Kb)
  • Retrieve 2JFF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JFF from S2C, [Save to disk]
  • Re-refined 2jff structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2JFF 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 2JFF
  • 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 2JFF, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2jff_A] [2jff]
  • SWISS-PROT database: [P14900]
  • Domain organization of [MURD_ECOLI] by SWISSPFAM
  • Other resources with information on 2JFF
  • Community annotation for 2JFF 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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