3I9G

Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragment in complex with sphingosine-1-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 3I9G

Classification: IMMUNE SYSTEM

Total Structure Weight: 48051.25

Macromolecule Entities
Molecule Chains Length Organism Details
Sonepcizumab antibody Fab fragment, heavy chain H 222 Mus musculus Fragment: Fab Fragment
Sonepcizumab antibody Fab fragment, light chain L 213 Mus musculus Fragment: Fab Fragment

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
S1P
Query on S1P

L (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en- 1-yl dihydrogen phosphate
sphingosine 1-phosphate (Synonym)
C18 H38 N O5 P
DUYSYHSSBDVJSM-KRWOKUGFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

L CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

L MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
S1P N/A in BindingDB
Kd: 1.1 nM  BindingMOAD
Kd: 1.1 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.190
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 66.05 α = 90.00
b = 70.89 β = 90.00
c = 138.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-10
  • Released Date: 2009-09-29
  • Deposition author(s): Huxford, T.

Revision History

  • 2011-07-13
    Type: Version format compliance