Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 41361.55 
• Atom Count: 2736 
• Residue Count: 355 
• Unique protein chains: 1

1ZW5

X-ray structure of Farnesyl diphosphate synthase protein

• DOI: 10.2210/pdb1ZW5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2005-06-03 Released: 2005-06-28 
• Deposition Author(s): Kavanagh, K.L., Guo, K., Wu, X., von Delft, F., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.223 
• R-Value Work: 0.172 

Literature

The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs.

Kavanagh, K.L., Guo, K., Dunford, J.E., Wu, X., Knapp, S., Ebetino, F.H., Rogers, M.J., Russell, R.G., Oppermann, U.

(2006) Proc.Natl.Acad.Sci.USA 103: 7829-7834

• PubMed: 16684881 
• DOI: 10.1073/pnas.0601643103
• Primary Citation of Related Structures:  
  1YV5


• PubMed Abstract: 
  

Osteoporosis and low bone mass are currently estimated to be a major public health risk affecting >50% of the female population over the age of 50. Because of their bone-selective pharmacokinetics, nitrogen-containing bisphosphonates (N-BPs), currently used as clinical inhibitors of bone-resorption diseases, target osteoclast farnesyl pyrophosphate synthase (FPPS) and inhibit protein prenylation. FPPS, a key branchpoint of the mevalonate pathway, catalyzes the successive condensation of isopentenyl pyrophosphate with dimethylallyl pyrophosphate and geranyl pyrophosphate. To understand the molecular events involved in inhibition of FPPS by N-BPs, we used protein crystallography, enzyme kinetics, and isothermal titration calorimetry. We report here high-resolution x-ray structures of the human enzyme in complexes with risedronate and zoledronate, two of the leading N-BPs in clinical use. These agents bind to the dimethylallyl/geranyl pyrophosphate ligand pocket and induce a conformational change. The interactions of the N-BP cyclic nitrogen with Thr-201 and Lys-200 suggest that these inhibitors achieve potency by positioning their nitrogen in the proposed carbocation-binding site. Kinetic analyses reveal that inhibition is competitive with geranyl pyrophosphate and is of a slow, tight binding character, indicating that isomerization of an initial enzyme-inhibitor complex occurs with inhibitor binding. Isothermal titration calorimetry indicates that binding of N-BPs to the apoenzyme is entropy-driven, presumably through desolvation entropy effects. These experiments reveal the molecular binding characteristics of an important pharmacological target and provide a route for further optimization of these important drugs.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
farnesyl diphosphate synthase	A	355	Homo sapiens	Mutation(s): 0  Gene Names: FDPS (FPS, KIAA1293) EC: 2.5.1.10
Find proteins for P14324 (Homo sapiens) Go to Gene View: FDPS Go to UniProtKB:  P14324

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IPE	A	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE ISOPENTENYL PYROPHOSPHATE C5 H12 O7 P2 NUHSROFQTUXZQQ-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
ZOL	A	ZOLEDRONIC ACID (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID C5 H10 N2 O7 P2 XRASPMIURGNCCH-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ZOL	Ki: 0.1 - 85.9 nM (99) BINDINGDB
ZOL	IC50: 0.2 - 475.3 nM (99) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.223 
• R-Value Work: 0.172 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 112.255	α = 90.00
b = 112.255	β = 90.00
c = 63.245	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	data scaling
MOSFLM	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-03 
• Released Date: 2005-06-28 
• Deposition Author(s): Kavanagh, K.L., Guo, K., Wu, X., von Delft, F., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2005-06-28
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2013-05-22
  Type: Non-polymer description
• Version 1.4: 2017-10-11
  Type: Refinement description
• Version 1.5: 2018-01-31
  Type: Structure summary