3CMD

Crystal structure of peptide deformylase from VRE-E.faecium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure.

Nam, K.H.Ham, J.I.Priyadarshi, A.Kim, E.E.Chung, N.Hwang, K.Y.

(2009) Proteins 74: 261-265


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
A, B
196Enterococcus faeciumMutation(s): 0 
Gene Names: def (def_2)
EC: 3.5.1.88
Find proteins for Q842S4 (Enterococcus faecium)
Go to UniProtKB:  Q842S4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

Download SDF File 
Download CCD File 
A, B
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 149.470α = 90.00
b = 149.470β = 90.00
c = 143.329γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data scaling
CNSrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-03-21 
  • Released Date: 2009-01-13 
  • Deposition Author(s): Hwang, K.Y., Nam, K.H.

Revision History 

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance