4E9A

Structure of Peptide Deformylase form Helicobacter Pylori in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Identification of Novel Peptide Deformylase Inhibitors from Natural Products

Cui, K., Zhu, L., Lu, W., Huang, J.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylase 11181Helicobacter pyloriMutation(s): 0 
Gene Names: def, def11
EC: 3.5.1.88
UniProt
Find proteins for Q672W7 (Helicobacter pylori)
Explore Q672W7 
Go to UniProtKB:  Q672W7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ672W7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QAP
Query on QAP
Download Ideal Coordinates CCD File 
C [auth A]2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
C17 H16 O4
SWUARLUWKZWEBQ-VQHVLOKHSA-N
EPE
Query on EPE
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D [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
DMS
Query on DMS
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CO
Query on CO
Download Ideal Coordinates CCD File 
B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.891α = 90
b = 52.057β = 90
c = 92.064γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description