3IMG

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.8 Ang resolution in a ternary complex with fragment compounds 5-methoxyindole and 1-benzofuran-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase.

Hung, A.W.Silvestre, H.L.Wen, S.Ciulli, A.Blundell, T.L.Abell, C.

(2009) Angew.Chem.Int.Ed.Engl. 48: 8452-8456


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pantothenate synthetase
A, B
301Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 2 
Gene Names: panC
EC: 6.3.2.1
Find proteins for P9WIL5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WIL5
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BZ2
Query on BZ2

Download SDF File 
Download CCD File 
A, B
1-benzofuran-2-carboxylic acid
C9 H6 O3
OFFSPAZVIVZPHU-UHFFFAOYSA-N
 Ligand Interaction
BZ3
Query on BZ3

Download SDF File 
Download CCD File 
A, B
5-methoxy-1H-indole
C9 H9 N O
DWAQDRSOVMLGRQ-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BZ2Kd: 1000000 nM (99) BINDINGDB
BZ3Kd: 1100000 nM (99) BINDINGDB
BZ3Kd: 1100000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.480α = 90.00
b = 71.220β = 99.40
c = 81.800γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description