5UPG

Crystal structure of LpxC from Pseudomonas aeruginosa in complex with PF-5081090


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of LpxC from Pseudomonas aeruginosa in complex with PF-5081090

Phan, J.N.Delker, S.L.Lorimer, D.D.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylase304Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lpxC
EC: 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47205
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8GJ
Query on 8GJ

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
(2R)-4-[4-(2-fluoro-4-methoxyphenyl)-2-oxopyridin-1(2H)-yl]-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide
C18 H21 F N2 O6 S
DNVUWHWBCMGQLU-GOSISDBHSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/M35UPG
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.84α = 111.27
b = 47.4β = 109.12
c = 48.15γ = 98.12
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
Cootmodel building
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description