3EON

2.55A crystal structure of native glutaryl-coa dehydrogenase from Burkholderia pseudomallei in complex with a small molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening.

Begley, D.W.Davies, D.R.Hartley, R.C.Hewitt, S.N.Rychel, A.L.Myler, P.J.Van Voorhis, W.C.Staker, B.L.Stewart, L.J.

(2011) Acta Crystallogr.,Sect.F 67: 1060-1069

  • DOI: 10.1107/S1744309111014436
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this d ...

    Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA. dbegley@embios.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutaryl-CoA dehydrogenase
A, B, C, D
396Burkholderia pseudomallei (strain 1710b)Mutation(s): 0 
EC: 1.3.8.6
Find proteins for Q3JP94 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JP94
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
341
Query on 341

Download SDF File 
Download CCD File 
C
(3,5-difluorophenyl)methanol
C7 H6 F2 O
LOGIHEKXJKHXEC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 97.409α = 90.00
b = 106.169β = 90.00
c = 144.185γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-09-21
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Refinement description