1YV5

Human farnesyl diphosphate synthase complexed with Mg and risedronate

Structural Biology Knowledgebase: 1YV5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YV5

Classification: Transferase

Total Structure Weight: 43560.18

Macromolecule Entities
Molecule Chains Length Organism Details
Farnesyl pyrophosphate synthetase A 374 Homo sapiens EC#: 2.5.1.10 IUBMB
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
RIS
Query on RIS

A 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID
C7 H11 N O7 P2
IIDJRNMFWXDHID-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RIS IC50: 0.36 - 860 nM (99) BindingDB
Ki: 0.36 - 82.2 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.205
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.95 α = 90.00
b = 110.95 β = 90.00
c = 70.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-15
  • Released Date: 2005-03-01
  • Deposition author(s): Kavanagh, K.L., Guo, K., Von Delft, F., Arrowsmith, C., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4