3IBA

Crystal structure of the complex of Trypanosoma cruzi farnesyl diphosphate synthase with zoledronate, IPP and Mg2+

Structural Biology Knowledgebase: 3IBA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.225

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3IBA

Classification: TRANSFERASE

Total Structure Weight: 41912.81

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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZOL
Query on ZOL

A ZOLEDRONIC ACID
(1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID (Synonym)
C5 H10 N2 O7 P2
XRASPMIURGNCCH-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)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.225
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.34 α = 90.00
b = 58.34 β = 90.00
c = 390.40 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-15
  • Released Date: 2010-02-09
  • Deposition author(s): Amzel, L.M., Huang, C.H., Gabelli, S.B., Oldfield, E.

Revision History

  • 2013-04-17
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4