1YQ7

Human farnesyl diphosphate synthase complexed with risedronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Human farnesyl diphosphate complexed with clinical inhibitor risedronate

Kavanagh, K.L.Guo, K.Oppermann, U.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthetaseA374Homo sapiensMutation(s): 0 
Gene Names: FDPSFPSKIAA1293
EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (UniProt)
Find proteins for P14324 (Homo sapiens)
Explore P14324 
Go to UniProtKB:  P14324
NIH Common Fund Data Resources
PHAROS  P14324
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIS
Query on RIS

Download CCD File 
A
1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID
C7 H11 N O7 P2
IIDJRNMFWXDHID-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RISKi:  82.19999694824219   nM  BindingDB
RISKi :  82.19999694824219   nM  PDBBind
RISIC50:  5.199999809265137   nM  BindingDB
RISIC50:  11   nM  BindingDB
RISIC50:  170   nM  BindingDB
RISIC50:  10   nM  BindingDB
RISIC50:  5.699999809265137   nM  BindingDB
RISIC50:  452.8999938964844   nM  BindingDB
RISKi:  0.36000001430511475   nM  BindingDB
RISIC50:  860   nM  BindingDB
RISIC50:  200   nM  BindingDB
RISKi:  16   nM  BindingDB
RISIC50:  6   nM  BindingDB
RISIC50:  0.36000001430511475   nM  BindingDB
RISIC50:  82   nM  BindingDB
RISIC50:  300   nM  BindingDB
RISIC50:  70   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.946α = 90
b = 110.946β = 90
c = 70.264γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Structure summary