4DWB

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

Structural Biology Knowledgebase: 4DWB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.218

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DWB

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 42094.04

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

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0M7
Query on 0M7

A [2-(pentylamino)ethane-1,1-diyl]bis(phosphonic acid)
C7 H19 N O6 P2
YDYMUJPNPOBLGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPE
Query on IPE

A 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
ISOPENTENYL PYROPHOSPHATE (Synonym)
C5 H12 O7 P2
NUHSROFQTUXZQQ-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 %)
0M7 IC50: 1840 nM (99) BindingDB

IC50: 1840 nM  BindingMOAD
IC50: 1840 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.218
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.87 α = 90.00
b = 57.87 β = 90.00
c = 392.44 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

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