S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-261

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases

Guo, R.T.Cao, R.Liang, P.H.Ko, T.P.Chang, T.H.Hudock, M.P.Jeng, W.Y.Chen, C.K.-M.Zhang, Y.Song, Y.Kuo, C.J.Yin, F.Oldfield, E.Wang, A.H.-J.

(2007) Proc Natl Acad Sci U S A 104: 10022-10027

  • DOI: https://doi.org/10.1073/pnas.0702254104
  • Primary Citation of Related Structures:  
    2E8T, 2E8U, 2E8V, 2E8W, 2E8X, 2E90, 2E91, 2E92, 2E93, 2E94, 2E95, 2E98, 2E99, 2E9A, 2E9C, 2E9D

  • PubMed Abstract: 

    Bisphosphonate drugs (e.g., Fosamax and Zometa) are thought to act primarily by inhibiting farnesyl diphosphate synthase (FPPS), resulting in decreased prenylation of small GTPases. Here, we show that some bisphosphonates can also inhibit geranylgeranyl diphosphate synthase (GGPPS), as well as undecaprenyl diphosphate synthase (UPPS), a cis-prenyltransferase of interest as a target for antibacterial therapy. Our results on GGPPS (10 structures) show that there are three bisphosphonate-binding sites, consisting of FPP or isopentenyl diphosphate substrate-binding sites together with a GGPP product- or inhibitor-binding site. In UPPS, there are a total of four binding sites (in five structures). These results are of general interest because they provide the first structures of GGPPS- and UPPS-inhibitor complexes, potentially important drug targets, in addition to revealing a remarkably broad spectrum of binding modes not seen in FPPS inhibition.

  • Organizational Affiliation

    Taiwan International Graduate Program, Institute of Biological Chemistry, Core Facility for Protein Crystallography, Academia Sinica, Taipei 115, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthetase
A, B
340Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12051 
Go to UniProtKB:  Q12051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12051
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.871α = 90
b = 116.051β = 90
c = 127.733γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description