3PN3

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with inhibitor 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis.

Fieulaine, S.Boularot, A.Artaud, I.Desmadril, M.Dardel, F.Meinnel, T.Giglione, C.

(2011) PLoS Biol 9: e1001066-e1001066

  • DOI: 10.1371/journal.pbio.1001066
  • Primary Citation of Related Structures:  
    3PN2, 3PN3, 3PN4, 3PN5, 3PN6, 3O3J, 3M6O, 3M6P, 3M6Q, 3M6R

  • PubMed Abstract: 
  • For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state ...

    For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.


    Organizational Affiliation

    CNRS, ISV, UPR2355, Gif-sur-Yvette, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide deformylase 1B, chloroplasticA, B193Arabidopsis thalianaMutation(s): 0 
Gene Names: DEF2PDF1BAt5g14660T15N1_150
EC: 3.5.1.88
Find proteins for Q9FUZ2 (Arabidopsis thaliana)
Explore Q9FUZ2 
Go to UniProtKB:  Q9FUZ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PN3
Query on PN3

Download Ideal Coordinates CCD File 
C [auth A], L [auth B]tert-butyl {(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl}carbamate
C15 H22 N2 O4
WLOCWKYZMRXKHU-ZDUSSCGKSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PN3Ki:  400   nM  Binding MOAD
PN3Ki :  400   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.6α = 90
b = 55.61β = 90
c = 149.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description