3P3E

Crystal Structure of the PSEUDOMONAS AERUGINOSA LpxC/LPC-009 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.182

Literature

Macromolecules
Sequence Display for 3P3E

Classification: HYDROLASE

Total Structure Weight: 35212.93

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase A 299 Pseudomonas aeruginosa EC#: 3.5.1 IUBMB
Fragment: UNP residues 1-299
Mutation: C40S
Gene Name(s): lpxC envA PA4406
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3P3 Kd: 8.35 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.182
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 52.64 α = 90.00
b = 73.61 β = 90.00
c = 88.31 γ = 90.00

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

  • Version 1_0: 2011-01-05

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2017-11-08

    Type: Advisory, Refinement description