4FW6

Crystal Structure of the LpxC in complex with N-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of the LpxC

Kang, Y.N.Stuckey, J.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseABCD302Pseudomonas aeruginosa PAO1Mutation(s): 1 
Gene Names: envAlpxCPA4406
EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P47205 
Go to UniProtKB:  P47205
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L59
Query on L59

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A, B, C, D
N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-(phenylethynyl)benzamide
C19 H18 N2 O4
SFYISUPIFOZKLQ-DYVFJYSZSA-N
 Ligand Interaction
PEG
Query on PEG

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A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L59Kd:  20.100000381469727   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.477α = 90
b = 89.63β = 90.08
c = 169.997γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description