2JFH

Crystal structure of MurD ligase in complex with L-Glu containing sulfonamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.214

Literature

Macromolecules
Sequence Display for 2JFH

Classification: LIGASE

Total Structure Weight: 48484.91

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-N-ACETYLMURAMOYL-ALANINE-D-GLUTAMATE LIGASE A 445 Escherichia coli EC#: 6.3.2.9 IUBMB
Details: INHIBITOR N-(6-BUTOXY-NAPHTHALENE-2-SULFONYL)-L-GLUTAMIC ACID BOUND
Gene Name(s): murD b0088 JW0086
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LK1
Query on LK1

A N-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-L-GLUTAMIC ACID
C19 H23 N O7 S
UAGYXJBYAFGRFR-KRWDZBQOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LK1 IC50: 710000 nM (100) BindingDB

Ki: 240000 nM  BindingMOAD
Ki: 870000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.214
  • Space Group: P 41

Unit Cell:

Length (Å) Angle (°)
a = 65.59 α = 90.00
b = 65.59 β = 90.00
c = 135.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-01
  • Released Date: 2007-05-15
  • Deposition author(s): Kotnik, M., Humljan, J., Contreras-Martel, C., Oblak, M., Kristan, K., Herve, M., Blanot, D., Urleb, U., Gobec, S., Dessen, A., Solmajer, T.

Revision History

  • 2011-05-08
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance