3VJC

Crystal structure of the human squalene synthase in complex with zaragozic acid A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase

Liu, C.I.Jeng, W.Y.Chang, W.J.Ko, T.P.Wang, A.H.J.

(2012) J Biol Chem 287: 18750-18757

  • DOI: https://doi.org/10.1074/jbc.M112.351254
  • Primary Citation of Related Structures:  
    3VJ8, 3VJ9, 3VJA, 3VJB, 3VJC, 3VJD, 3VJE

  • PubMed Abstract: 

    Zaragozic acids (ZAs) belong to a family of fungal metabolites with nanomolar inhibitory activity toward squalene synthase (SQS). The enzyme catalyzes the committed step of sterol synthesis and has attracted attention as a potential target for antilipogenic and antiinfective therapies. Here, we have determined the structure of ZA-A complexed with human SQS. ZA-A binding induces a local conformational change in the substrate binding site, and its C-6 acyl group also extends over to the cofactor binding cavity. In addition, ZA-A effectively inhibits a homologous bacterial enzyme, dehydrosqualene synthase (CrtM), which synthesizes the precursor of staphyloxanthin in Staphylococcus aureus to cope with oxidative stress. Size reduction at Tyr(248) in CrtM further increases the ZA-A binding affinity, and it reveals a similar overall inhibitor binding mode to that of human SQS/ZA-A except for the C-6 acyl group. These structures pave the way for further improving selectivity and development of a new generation of anticholesterolemic and antimicrobial inhibitors.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Squalene synthase
A, B, C, D, E
A, B, C, D, E, F
343Homo sapiensMutation(s): 0 
Gene Names: FDFT1
EC: 2.5.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P37268 (Homo sapiens)
Explore P37268 
Go to UniProtKB:  P37268
PHAROS:  P37268
GTEx:  ENSG00000079459 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37268
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZGA
Query on ZGA

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
L [auth C]
N [auth D]
Q [auth E]
G [auth A],
I [auth B],
L [auth C],
N [auth D],
Q [auth E],
S [auth F]
Zaragozic acid A
C35 H46 O14
DFKDOZMCHOGOBR-NCSQYGPNSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
M [auth C]
O [auth D]
R [auth E]
H [auth A],
J [auth B],
M [auth C],
O [auth D],
R [auth E],
T [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth B],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZGA PDBBind:  3VJC Kd: 18.9 (nM) from 1 assay(s)
BindingDB:  3VJC IC50: min: 0.5, max: 12 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.873α = 90
b = 153.153β = 91.72
c = 91.855γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary