4E9A

Structure of Peptide Deformylase form Helicobacter Pylori in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.662 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase 11
A
181Helicobacter pyloriGene Names: def
EC: 3.5.1.88
Find proteins for Q672W7 (Helicobacter pylori)
Go to UniProtKB:  Q672W7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
QAP
Query on QAP

Download SDF File 
Download CCD File 
A
2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
C17 H16 O4
SWUARLUWKZWEBQ-VQHVLOKHSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.662 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.891α = 90.00
b = 52.057β = 90.00
c = 92.064γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release