3M6P

Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with actinonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1371/journal.pbio.1001066
  • Primary Citation of Related Structures:  
    3M6O, 3M6P, 3M6Q, 3M6R, 3O3J, 3PN2, 3PN3, 3PN4, 3PN5, 3PN6

  • 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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylase 1B
A, B
193Arabidopsis thalianaMutation(s): 0 
Gene Names: def
EC: 3.5.1.88
UniProt
Find proteins for Q9FUZ2 (Arabidopsis thaliana)
Explore Q9FUZ2 
Go to UniProtKB:  Q9FUZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FUZ2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BB2
Query on BB2

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
ACTINONIN
C19 H35 N3 O5
XJLATMLVMSFZBN-VYDXJSESSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BB2 Binding MOAD:  3M6P Ki: 0.9 (nM) from 1 assay(s)
PDBBind:  3M6P Kd: 4.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.56α = 90
b = 56.47β = 90
c = 145.95γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
REFMACrefinement
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description