1YHM

Structure of the complex of Trypanosoma cruzi farnesyl disphosphate synthase with alendronate, Isopentenyl diphosphate and mg+2

Structural Biology Knowledgebase: 1YHM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YHM

Classification: TRANSFERASE

Total Structure Weight: 127767.99

Macromolecule Entities
Molecule Chains Length Organism Details
farnesyl pyrophosphate synthase A, B, C 362 Trypanosoma cruzi EC#: 2.5.1.10 IUBMB
Mutation: M4M, M39M, M40M, M53M, M86M, M101M, M106M, M138M, M168M, M174M, M188M, M219M, M232M, M253M
Gene Name(s):

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
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)
AHD
Query on AHD

A, B, C 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE
ALENDRONATE, FOSAMAX (TM) (Synonym)
C4 H9 N O7 P2
OGSPWJRAVKPPFI-UHFFFAOYSA-J
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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 %)
AHD N/A in BindingDB
IC50: 147000 nM  BindingMOAD
IC50: 147000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.208
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 103.21 α = 90.00
b = 103.21 β = 90.00
c = 385.24 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-09
  • Released Date: 2005-12-20
  • Deposition author(s): Gabelli, S.B., McLellan, J.S., Montalvetti, A., Oldfield, E., Docampo, R., Amzel, L.M.

Revision History

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