6I0R

Structure of quinolinate synthase in complex with 5-mercaptopyridine-2,3-dicarboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design of specific inhibitors of quinolinate synthase based on [4Fe-4S] cluster coordination.

Saez Cabodevilla, J.Volbeda, A.Hamelin, O.Latour, J.M.Gigarel, O.Clemancey, M.Darnault, C.Reichmann, D.Amara, P.Fontecilla-Camps, J.C.Ollagnier de Choudens, S.

(2019) Chem Commun (Camb) 55: 3725-3728

  • DOI: https://doi.org/10.1039/c8cc09023h
  • Primary Citation of Related Structures:  
    6I0K, 6I0P, 6I0R

  • PubMed Abstract: 

    Quinolinate synthase (NadA) is a [4Fe-4S] cluster-containing enzyme involved in the formation of quinolinic acid, the precursor of the essential NAD coenzyme. Here, we report the synthesis and activity of derivatives of the first inhibitor of NadA. Using multidisciplinary approaches we have investigated their action mechanism and discovered additional specific inhibitors of this enzyme.


  • Organizational Affiliation

    Univ. Grenoble Alpes, CEA, CNRS, BIG-LCBM, UMR5249, 38000, Grenoble, France. sollagnier@cea.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Quinolinate synthase A305Thermotoga maritima MSB8Mutation(s): 2 
Gene Names: nadATM_1644
EC: 2.5.1.72
UniProt
Find proteins for Q9X1X7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1X7 
Go to UniProtKB:  Q9X1X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1X7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QAT
Query on QAT

Download Ideal Coordinates CCD File 
J [auth A]5-mercaptopyridine-2,3-dicarboxylic acid
C7 H5 N O4 S
XCYZNZIVHOIFRT-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
F [auth A],
G [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
H2S
Query on H2S

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth A],
I [auth A]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.9α = 90
b = 48.5β = 107.1
c = 60.5γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FranceANR-16-CE18-0026

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description