1BSJ

COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural basis for the design of antibiotics targeting peptide deformylase.

Hao, B., Gong, W., Rajagopalan, P.T., Zhou, Y., Pei, D., Chan, M.K.

(1999) Biochemistry 38: 4712-4719

  • DOI: 10.1021/bi982594c
  • Primary Citation of Related Structures:  
    1BSJ, 1BSK

  • PubMed Abstract: 

    • While protein synthesis in bacteria begins with a formylated methionine, the formyl group of the nascent polypeptide is removed by peptide deformylase. Since eukaryotic protein synthesis does not involve formylation and deformylation at the N-terminus, there has been increasing interest in peptide deformylase as a potential target for antibacterial chemotherapy ...

    While protein synthesis in bacteria begins with a formylated methionine, the formyl group of the nascent polypeptide is removed by peptide deformylase. Since eukaryotic protein synthesis does not involve formylation and deformylation at the N-terminus, there has been increasing interest in peptide deformylase as a potential target for antibacterial chemotherapy. Toward this end and to aid in the design of effective antibiotics targeting peptide deformylase, the structures of the protein-inhibitor complexes of both the cobalt and the zinc containing Escherichia coli peptide deformylase bound to the transition-state analogue, (S)-2-O-(H-phosphonoxy)-L-caproyl-L-leucyl-p-nitroanilide (PCLNA), have been determined. The proteins for both deformylase-inhibitor complexes show basically the same fold as for the native enzyme. The PCLNA inhibitor adopts an extended conformation and fits nicely into a hydrophobic cavity located near the metal site. On the basis of these structures, guidelines for the design of high-affinity deformylase inhibitors are suggested. As our results show that the protein residues which interact with the PCLNA inhibitor are conserved over a wide variety of species, we suggest that antibiotics targeting deformylase could have wide applicability.

    Related Citations: 
    • Crystal Structure of the Escherichia Coli Peptide Deformylase
      Chan, M.K., Gong, W., Rajagopalan, P.T., Hao, B., Tsai, C., Pei, D.
      (1997) Biochemistry 36: 13904
    Organizational Affiliation: 

    Departments of Biochemistry and Chemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PEPTIDE DEFORMYLASE)A168Escherichia coliMutation(s): 0 
EC: 3.5.1.27 (PDB Primary Data), 3.5.1.88 (UniProt)
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Explore P0A6K3 
Go to UniProtKB:  P0A6K3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6K3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLN
Query on MLN
Download Ideal Coordinates CCD File 
D [auth A](S)-2-(PHOSPHONOXY)CAPROYL-L-LEUCYL-P-NITROANILIDE
C18 H28 N3 O8 P
HARXAJAHMRMERT-HOTGVXAUSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
CO
Query on CO
Download Ideal Coordinates CCD File 
B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.08α = 90
b = 99.08β = 90
c = 111.04γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description