2WGG

Crystal Structure of Mycobacterium tuberculosis C171Q KasA variant with bound TLM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structures of Mycobacterium Tuberculosis Kasa Show Mode of Action within Cell Wall Biosynthesis and its Inhibition by Thiolactomycin

Luckner, S.R.Machutta, C.A.Tonge, P.J.Kisker, C.

(2009) Structure 17: 1004

  • DOI: 10.1016/j.str.2009.04.012
  • Primary Citation of Related Structures:  
    2WGD, 2WGE, 2WGF, 2WGG

  • PubMed Abstract: 
  • Mycobacteria have a unique cell wall consisting of mycolic acids, very-long-chain lipids that provide protection and allow the bacteria to persist within human macrophages. Inhibition of cell wall biosynthesis is fatal for the organism and a starting point for the discovery and development of novel antibiotics ...

    Mycobacteria have a unique cell wall consisting of mycolic acids, very-long-chain lipids that provide protection and allow the bacteria to persist within human macrophages. Inhibition of cell wall biosynthesis is fatal for the organism and a starting point for the discovery and development of novel antibiotics. We determined the crystal structures of KasA, a key enzyme involved in the biosynthesis of long-chain fatty acids, in its apo-form and bound to the natural product inhibitor thiolactomycin. Detailed insights into the interaction of the inhibitor with KasA and the identification of a polyethylene glycol molecule that mimics a fatty acid substrate of approximately 40 carbon atoms length, represent the first atomic view of a mycobacterial enzyme involved in the synthesis of long-chain fatty acids and provide a robust platform for the development of novel thiolactomycin analogs with high affinity for KasA.


    Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
416Mycobacterium tuberculosisMutation(s): 1 
EC: 2.3.1.41 (PDB Primary Data), 2.3.1.293 (UniProt)
UniProt
Find proteins for P9WQD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQD9 
Go to UniProtKB:  P9WQD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQD9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
BA [auth E],
FA [auth F],
GA [auth G],
K [auth A],
M [auth B],
BA [auth E],
FA [auth F],
GA [auth G],
K [auth A],
M [auth B],
MA [auth H],
U [auth C],
Y [auth D]
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
TLM
Query on TLM

Download Ideal Coordinates CCD File 
CA [auth F],
I [auth A],
IA [auth G],
KA [auth H],
N [auth B],
CA [auth F],
I [auth A],
IA [auth G],
KA [auth H],
N [auth B],
S [auth C],
W [auth D],
Z [auth E]
THIOLACTOMYCIN
C11 H14 O2 S
SYQNUQSGEWNWKV-XUIVZRPNSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth F],
HA [auth G],
L [auth A],
P [auth B],
Q [auth B],
EA [auth F],
HA [auth G],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
V [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth E],
DA [auth F],
J [auth A],
JA [auth G],
LA [auth H],
AA [auth E],
DA [auth F],
J [auth A],
JA [auth G],
LA [auth H],
O [auth B],
T [auth C],
X [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TLM BindingDB:  2WGG Ki: min: 1900, max: 1.75e+5 (nM) from 2 assay(s)
Kd: 2.26e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.276α = 90
b = 151.276β = 90
c = 147.96γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
TRUNCATEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance