4KPD

Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb4KPD/pdb

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


• Deposited: 2013-05-13 Released: 2014-04-30 
• Deposition Author(s): Barnett, B.L., Tsoumpra, M.K., Muniz, J.R.C., Walter, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate

Tsoumpra, M.K., Muniz, J.R.C., Barnett, B.L., Pilka, E., Kwaasi, A., Kavanagh, K.L., Evdokimov, A.G., Walter, R.L., Ebetino, F.H., 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: 43.73 kDa 
• Atom Count: 2,991 
• Modelled Residue Count: 341 
• 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	F [auth A]	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID C7 H11 N O7 P2 IIDJRNMFWXDHID-UHFFFAOYSA-N
IPE	E [auth A]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C5 H12 O7 P2 NUHSROFQTUXZQQ-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RIS	BindingDB:  4KPD	Ki: min: 0.36, max: 82.2 (nM) from 3 assay(s)
		IC50: min: 0.36, max: 860 (nM) from 14 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.73	α = 90
b = 111.73	β = 90
c = 66.99	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Barnett, B.L., Tsoumpra, M.K., Muniz, J.R.C., Walter, R.L.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary