3CP6 | pdb_00003cp6

Crystal structure of human farnesyl diphosphate synthase (T201A mutant) complexed with Mg and biphosphonate inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3CP6/pdb

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


• Deposited: 2008-03-31 Released: 2008-04-15 
• Deposition Author(s): Pilka, E.S., Dunford, J.E., Guo, K., Pike, A.C.W., von Delft, F., Barnett, B.L., Ebetino, F.H., Arrowsmith, C.H., Bountra, C., 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: 
  0.243 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Human farnesyl diphosphate synthase (T201A mutant) complexed with Mg and biphosphonate inhibitor.

Pilka, E.S., Dunford, J.E., Guo, K., Pike, A.C.W., von Delft, F., Barnett, B.L., Ebetino, F.H., Arrowsmith, C.H., Bountra, C., 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: 43.6 kDa 
• Atom Count: 2,901 
• Modeled Residue Count: 334 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthetase	A	376	Homo sapiens	Mutation(s): 1  Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.1 (PDB Primary Data), 2.5.1.10 (PDB Primary Data)
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
RSX	E [auth A]	(4aS,7aR)-octahydro-1H-cyclopenta[b]pyridine-6,6-diylbis(phosphonic acid) C8 H17 N O6 P2 JWOKHNWVYMHFTC-NKWVEPMBSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.243 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.531	α = 90
b = 112.531	β = 90
c = 62.919	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Pilka, E.S., Dunford, J.E., Guo, K., Pike, A.C.W., von Delft, F., Barnett, B.L., Ebetino, F.H., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Russell, R.G.G., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-02-01
  Changes: Database references
• Version 1.5: 2023-09-20
  Changes: Data collection, Refinement description