5O0A

Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 5-methyl-1-phenyl-pyrazole-4-carboxylic acid (Fragment 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.805 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew.

Mendes, V.Kim, S.Y.Malhotra, S.Ochoa-Montano, B.Blaszczyk, M.Blundell, T.L.Thomas, S.E.

(2017) J. Mol. Biol. 429: 2677-2693

  • DOI: 10.1016/j.jmb.2017.06.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Interest in applications of protein crystallography to medicine was evident, as the first high-resolution structures emerged in the 50s and 60s. In Cambridge, Max Perutz and John Kendrew sought to understand mutations in sickle cell and other genetic ...

    Interest in applications of protein crystallography to medicine was evident, as the first high-resolution structures emerged in the 50s and 60s. In Cambridge, Max Perutz and John Kendrew sought to understand mutations in sickle cell and other genetic diseases related to hemoglobin, while in Oxford, the group of Dorothy Hodgkin became interested in long-lasting zinc-insulin crystals for treatment of diabetes and later considered insulin redesign, as synthetic insulins became possible. The use of protein crystallography in structure-guided drug discovery emerged as enzyme structures allowed the identification of potential inhibitor-binding sites and optimization of interactions of hits using the structure of the target protein. Early examples of this approach were the use of the structure of renin to design antihypertensives and the structure of HIV protease in design of AIDS antivirals. More recently, use of structure-guided design with fragment-based drug discovery, which reduces the size of screening libraries by decreasing complexity, has improved ligand efficiency in drug design and has been used to progress three oncology drugs through clinical trials to FDA approval. We exemplify current developments in structure-guided target identification and fragment-based lead discovery with efforts to develop new antimicrobials for mycobacterial infections.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphopantetheine adenylyltransferase
A, B, C
162Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543)Mutation(s): 0 
Gene Names: coaD
EC: 2.7.7.3
Find proteins for B1MDL6 (Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543))
Go to UniProtKB:  B1MDL6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9FH
Query on 9FH

Download SDF File 
Download CCD File 
A, B, C
5-methyl-1-phenyl-pyrazole-4-carboxylic acid
C11 H10 N2 O2
USSMIQWDLWJQDQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.805 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.244α = 90.00
b = 125.247β = 90.00
c = 119.128γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cystic Fibrosis TrustUnited Kingdom--

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Database references