2F92

Crystal structure of human FPPS in complex with alendronate

Structural Biology Knowledgebase: 2F92 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.247

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2F92

Classification: TRANSFERASE

Total Structure Weight: 40720.42

Macromolecule Entities
Molecule Chains Length Organism Details
Farnesyl Diphosphate Synthase F 350 Homo sapiens EC#: 2.5.1.10 IUBMB
Fragment: Residues 6-353
Details: Includes: Dimethylallyltranstransferase; Geranyltranstransferase
Gene Name(s): FDPS Gene View FPS KIAA1293
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

F 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)
PO4
Query on PO4

F PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

F ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AHD IC50: 50 - 2249 nM (100) BindingDB
Ki: 44.2 - 393.1 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.247
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 111.50 α = 90.00
b = 111.50 β = 90.00
c = 70.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-05
  • Released Date: 2006-02-28
  • Deposition author(s): Rondeau, J.-M., Bitsch, F., Bourgier, E., Geiser, M., Hemmig, R., Kroemer, M., Lehmann, S., Ramage, P., Rieffel, S., Strauss, A., Green, J.R., Jahnke, W.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4