6PIB

Structure of the Klebsiella pneumoniae LpxH-AZ1 complex

  • Classification: BIOSYNTHETIC PROTEIN
  • Organism(s): Klebsiella pneumoniae
  • Expression System: Escherichia coli

  • Deposited: 2019-06-26 Released: 2020-02-12 
  • Deposition Author(s): Cho, J., Zhou, P.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics

Cho, J.Lee, M.Cochrane, C.Webster, C.Fenton, B.Zhao, J.Hong, J.Zhao, P.

(2020) Proc.Natl.Acad.Sci.USA --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-2,3-diacylglucosamine hydrolase
A
260Klebsiella pneumoniaeMutation(s): 0 
Gene Names: lpxH
EC: 3.6.1.54
Find proteins for A0A1S0WIC1 (Klebsiella pneumoniae)
Go to UniProtKB:  A0A1S0WIC1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
OKV
Query on OKV

Download SDF File 
Download CCD File 
A
1-[5-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)-2,3-dihydro-1H-indol-1-yl]ethan-1-one
C21 H22 F3 N3 O3 S
JRTCXCIMCOKGMN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.750α = 90.00
b = 106.750β = 90.00
c = 52.970γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-06-26 
  • Released Date: 2020-02-12 
  • Deposition Author(s): Cho, J., Zhou, P.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115355
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI139216

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release