6JFQ

K2U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

K2U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus

Lee, I.H.Ho, T.H.Kang, L.W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
A
184Staphylococcus aureusMutation(s): 0 
Gene Names: def (def1, pdf1)
EC: 3.5.1.88
Find proteins for P68826 (Staphylococcus aureus)
Go to UniProtKB:  P68826
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
K2U
Query on K2U

Download SDF File 
Download CCD File 
A
(3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid
C18 H20 O3 S
OBXQOECJZPGJTO-SJLPKXTDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 95.429α = 90.00
b = 120.699β = 90.00
c = 47.120γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release