1Q1Y

Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent

Yoon, H.J.Kim, H.L.Lee, S.K.Kim, H.W.Kim, H.W.Lee, J.Y.Mikami, B.Suh, S.W.

(2004) Proteins 57: 639-642


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
A
191Staphylococcus 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
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BB2
Query on BB2

Download SDF File 
Download CCD File 
A
ACTINONIN
2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE
C19 H35 N3 O5
XJLATMLVMSFZBN-VYDXJSESSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BB2IC50: <5 - 20 nM (99) BINDINGDB
BB2IC50: 20 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 94.417α = 90.00
b = 120.844β = 90.00
c = 48.057γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-02-08
    Type: Other, Version format compliance