3RYE | pdb_00003rye

Human FDPS Synthase in Complex with a N-Methyl Pyridinum Bisphosphonate

• PDB DOI: https://doi.org/10.2210/pdb3RYE/pdb

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


• Deposited: 2011-05-11 Released: 2011-06-01 
• Deposition Author(s): Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Human FDPS Synthase in Complex with a N-Methyl Pyridinum Bisphosphonate

Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

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: 40.58 kDa 
• Atom Count: 2,939 
• Modeled Residue Count: 341 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A	349	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
UNR	B [auth A]	3-(2-hydroxy-2,2-diphosphonoethyl)-1-methylpyridinium C8 H14 N O7 P2 BBNRLGQPSIXFHZ-UHFFFAOYSA-O
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
UNR	BindingDB:  3RYE	Ki: min: 3.9, max: 177 (nM) from 2 assay(s)
		IC50: min: 19.6, max: 1706 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.311	α = 90
b = 111.311	β = 90
c = 69.713	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description