4Q23

The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates

• PDB DOI: https://doi.org/10.2210/pdb4Q23/pdb

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


• Deposited: 2014-04-05 Released: 2015-03-18 
• Deposition Author(s): Tsoumpra, M.K., Muniz, J.R.C., Barnett, B.L., Kwaasi, A.A., Pilka, E.S., Kavanagh, K.L., Evdokimov, A., Walter, R.L., Ebetino, F.H., von Delft, F., Oppermann, U., Russell, R.G.G., Dunford, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.223 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates

Tsoumpra, M.K., Muniz, J.R.C., Barnett, B.L., Kwaasi, A.A., Pilka, E.S., Kavanagh, K.L., Evdokimov, A., Walter, R.L., Ebetino, F.H., von Delft, F., Oppermann, U., Russell, R.G.G., Dunford, J.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 (software)

Macromolecule Content

• Total Structure Weight: 43.57 kDa 
• Atom Count: 2,821 
• Modelled Residue Count: 337 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A	375	Homo sapiens	Mutation(s): 1  Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIS	B [auth A]	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID C7 H11 N O7 P2 IIDJRNMFWXDHID-UHFFFAOYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RIS	BindingDB:  4Q23	Ki: min: 0.36, max: 82.2 (nM) from 3 assay(s)
		IC50: min: 0.36, max: 860 (nM) from 13 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.223 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.36	α = 90
b = 111.36	β = 90
c = 67.6	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Tsoumpra, M.K., Muniz, J.R.C., Barnett, B.L., Kwaasi, A.A., Pilka, E.S., Kavanagh, K.L., Evdokimov, A., Walter, R.L., Ebetino, F.H., von Delft, F., Oppermann, U., Russell, R.G.G., Dunford, J.E.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description