3RYE

Human FDPS Synthase in Complex with a N-Methyl Pyridinum Bisphosphonate

Structural Biology Knowledgebase: 3RYE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RYE

Classification: TRANSFERASE

Total Structure Weight: 40584.32

Macromolecule Entities
Molecule Chains Length Organism Details
Farnesyl pyrophosphate synthase A 349 Homo sapiens EC#: 2.5.1.10 IUBMB
Mutation: Q5S
Gene Name(s): FDPS Gene View FPS KIAA1293

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

A 3-(2-hydroxy-2,2-diphosphonoethyl)-1-methylpyridinium
C8 H14 N O7 P2
BBNRLGQPSIXFHZ-UHFFFAOYSA-O
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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UNR IC50: 19.6 - 1706 nM (100) BindingDB
Ki: 3.9 - 177 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.185
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 111.31 α = 90.00
b = 111.31 β = 90.00
c = 69.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-11
  • Released Date: 2011-06-01
  • Deposition author(s): Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4