3P3G

Crystal Structure of the Escherichia coli LpxC/LPC-009 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.177
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 3P3G

Classification: HYDROLASE

Total Structure Weight: 34800.83

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase A 300 Escherichia coli EC#: 3.5.1 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3P3
Query on 3P3

A N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]- 4-(4-phenylbuta-1,3-diyn-1-yl)benzamide
C21 H18 N2 O4
VUYMSCCEGRLBAF-BEFAXECRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UKW
Query on UKW

A 4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide
C13 H12 N2 O4
JJXZDQZGPLQGCP-KCJUWKMLSA-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)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3P3 N/A in BindingDB
Ki: 0.18 nM  BindingMOAD
Ki: 0.18 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.177
  • R-Value Work: 0.155
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 106.72 α = 90.00
b = 106.72 β = 90.00
c = 52.68 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-10-04
  • Released Date: 2011-01-05
  • Deposition author(s): Lee, C.-J, Zhou, P.

Revision History

  • 2011-07-13
    Type: Version format compliance