4DXJ

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

Structural Biology Knowledgebase: 4DXJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DXJ

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 126307.29

Macromolecule Entities
Molecule Chains Length Organism Details
Farnesyl pyrophosphate synthase A, B, C 362 Trypanosoma cruzi EC#: 2.5.1.10 IUBMB
Gene Name(s):

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0M9
Query on 0M9

A, B, C [2-(propylamino)ethane-1,1-diyl]bis(phosphonic acid)
C5 H15 N O6 P2
YFFJUBPLIKXHAO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPE
Query on IPE

A, B, C 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
ISOPENTENYL PYROPHOSPHATE (Synonym)
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

B TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

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

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

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

A, B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0M9 IC50: 38 nM (99) BindingDB

IC50: 38 nM  BindingMOAD
IC50: 38.0 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.220
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.22 α = 90.00
b = 103.22 β = 90.00
c = 386.66 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-27
  • Released Date: 2013-01-16
  • Deposition author(s): Aripirala, S., Amzel, L.M., Gabelli, S.B.

Revision History

  • 2013-04-17
    Type: Non-polymer description | Details: relabeled ligand IPR to IPE