6IH0

Aquifex aeolicus LpxC complex with ACHN-975


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The Complex Structure of Protein AaLpxC from Aquifex aeolicus with ACHN-975 Molecule Suggests an Inhibitory Mechanism at Atomic-Level against Gram-Negative Bacteria

Fan, S.Li, D.Yan, M.Feng, X.Lv, G.Wu, G.Jin, Y.Wang, Y.Yang, Z.

(2021) Molecules 26


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylaseA279Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: lpxCenvAaq_1772
EC: 3.5.1.108
UniProt
Find proteins for O67648 (Aquifex aeolicus (strain VF5))
Explore O67648 
Go to UniProtKB:  O67648
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A5F (Subject of Investigation/LOI)
Query on A5F

Download Ideal Coordinates CCD File 
B [auth A]N-[(2S)-3-azanyl-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]-4-[4-[(1R,2R)-2-(hydroxymethyl)cyclopropyl]buta -1,3-diynyl]benzamide
C20 H23 N3 O4
GOCUUDXEOKIQRU-IXDOHACOSA-N
 Ligand Interaction
A5U (Subject of Investigation/LOI)
Query on A5U

Download Ideal Coordinates CCD File 
D [auth A]methyl (2S)-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate
C11 H22 N2 O4
UTWVEOUYCGZORL-SSDOTTSWSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.569α = 90
b = 65.569β = 90
c = 131.595γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81761128016
Other governmentChinaCAMS Innovation Fund for Medical Sciences(2016-12M-3-012)
Other governmentChinaCAMS Innovation Fund for Medical Sciences(2016-12M-3-022)
National Natural Science Foundation of ChinaChina81621064

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references, Derived calculations, Structure summary