3CMD

Crystal structure of peptide deformylase from VRE-E.faecium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylase
A, B
196Enterococcus faeciumMutation(s): 0 
EC: 3.5.1.88
UniProt
Find proteins for Q842S4 (Enterococcus faecium)
Explore Q842S4 
Go to UniProtKB:  Q842S4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ842S4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
P [auth B]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
J [auth B]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.47α = 90
b = 149.47β = 90
c = 143.329γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description