4DWG

Crystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-heptylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+

Structural Biology Knowledgebase: 4DWG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DWG

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 42101.12

Macromolecule Entities
Molecule Chains Length Organism Details
Farnesyl pyrophosphate synthase A 362 Trypanosoma cruzi EC#: 2.5.1.10 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0M8
Query on 0M8

A [2-(heptylamino)ethane-1,1-diyl]bis(phosphonic acid)
C9 H23 N O6 P2
WRMHTOUCTOHPIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0M8 IC50: 58 nM (99) BindingDB

IC50: 58 nM  BindingMOAD
IC50: 58.0 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.202
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.17 α = 90.00
b = 58.17 β = 90.00
c = 391.82 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-24
  • Released Date: 2013-01-16
  • Deposition author(s): Aripirala, S., Amzel, L.M., Gabelli, S.B.

Revision History

No revisions since initial release