2OPN

Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-527

• PDB DOI: https://doi.org/10.2210/pdb2OPN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-29 Released: 2007-10-02 
• Deposition Author(s): Cao, R., Gao, Y.G., Robinson, H., Goddard, A., Oldfield, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.298 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Starting Model: experimental

Literature

Bisphosphonates: Teaching Old Drugs with New Tricks

Zhang, Y., Cao, R., Leon, A., Guo, R.T., Krysiak, K., Yin, F., Hudock, M.P., Mukherjee, S., Gao, Y.G., Robinson, H., Song, Y., No, J.H., Hong, W., Morita, C., Wang, A.H.-J., Oldfield, E.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 43.54 kDa 
• Atom Count: 2,789 
• Modelled Residue Count: 336 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltranstransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.10)]	A	374	Homo sapiens	Mutation(s): 0  Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P14324 (Homo sapiens) Explore P14324  Go to UniProtKB:  P14324
PHAROS:  P14324 GTEx:  ENSG00000160752

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SUF	G [auth A]	[2-(DIMETHYL-LAMBDA~4~-SULFANYL)-1-HYDROXYETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID) C4 H14 O7 P2 S QRMZYUMGWARYEI-UHFFFAOYSA-N
PO4	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SUF	BindingDB:  2OPN	IC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.298 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.652	α = 90
b = 111.652	β = 90
c = 66.841	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Cao, R., Gao, Y.G., Robinson, H., Goddard, A., Oldfield, E.

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description