3B7L

Human farnesyl diphosphate synthase complexed with MG and minodronate

• PDB DOI: https://doi.org/10.2210/pdb3B7L/pdb

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


• Deposited: 2007-10-31 Released: 2007-11-13 
• Deposition Author(s): Pilka, E.S., Dunford, J.E., Guo, K., Pike, A.C.W., Kavanagh, K.L., von Delft, F., Ebetino, F.H., Arrowsmith, C.H., Edwards, A.M., Russell, R.G.G., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.202 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Human farnesyl diphosphate synthase complexed with MG and minodronate.

Pilka, E.S., Dunford, J.E., Guo, K., Pike, A.C.W., Kavanagh, K.L., von Delft, F., Ebetino, F.H., Arrowsmith, C.H., Edwards, A.M., Russell, R.G.G., Oppermann, U.

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 (software)

Macromolecule Content

• Total Structure Weight: 41.32 kDa 
• Atom Count: 3,041 
• Modelled Residue Count: 343 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthetase	A	356	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M0N	F [auth A]	(1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID) C9 H12 N2 O7 P2 VMMKGHQPQIEGSQ-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M0N	BindingDB:  3B7L	IC50: min: 1.9, max: 3 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.202 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.922	α = 90
b = 110.922	β = 90
c = 67.308	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Pilka, E.S., Dunford, J.E., Guo, K., Pike, A.C.W., Kavanagh, K.L., von Delft, F., Ebetino, F.H., Arrowsmith, C.H., Edwards, A.M., Russell, R.G.G., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description