3QCV

Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (18:2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Biochemical and structural characterization of lysophosphatidic Acid binding by a humanized monoclonal antibody.

Fleming, J.K.Wojciak, J.M.Campbell, M.A.Huxford, T.

(2011) J.Mol.Biol. 408: 462-476

  • DOI: 10.1016/j.jmb.2011.02.061
  • Primary Citation of Related Structures:  3QCT, 3QCU

  • PubMed Abstract: 
  • Lysophosphatidic acid (LPA) is a common product of glycerophospholipid metabolism and an important mediator of signal transduction. Aberrantly high LPA concentrations accompany multiple disease states. One potential approach for treatment of these di ...

    Lysophosphatidic acid (LPA) is a common product of glycerophospholipid metabolism and an important mediator of signal transduction. Aberrantly high LPA concentrations accompany multiple disease states. One potential approach for treatment of these diseases, therefore, is the therapeutic application of antibodies that recognize and bind LPA as their antigen. We have determined the X-ray crystal structure of an anti-LPA antibody (LT3015) Fab fragment in its antigen-free form to 2.15 Å resolution and in complex with two LPA isotypes (14:0 and 18:2) to resolutions of 1.98 and 2.51 Å, respectively. The variable CDR (complementarity-determining region) loops at the antigen binding site adopt nearly identical conformations in the free and antigen-bound crystal structures. The crystallographic models reveal that the LT3015 antibody employs both heavy- and light-chain CDR loops to create a network of eight hydrogen bonds with the glycerophosphate head group of its LPA antigen. The head group is almost completely excluded from contact with solvent, while the hydrocarbon tail is partially solvent-exposed. In general, mutation of amino acid residues at the antigen binding site disrupts LPA binding. However, the introduction of particular mutations chosen strategically on the basis of the structures can positively influence LPA binding affinity. Finally, these structures elucidate the exquisite specificity demonstrated by an anti-lipid antibody for binding a structurally simple and seemingly unconstrained target molecule.


    Organizational Affiliation

    Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LT3015 antibody Fab fragment, heavy chain
H, I
223N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LT3015 antibody Fab fragment, light chain
L, M
218N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
18L
Query on 18L

Download SDF File 
Download CCD File 
H, I
(2R)-2-hydroxy-3-(phosphonooxy)propyl (9Z,12Z)-octadeca-9,12-dienoate
D (+)-sn-1-O-linoleoyl-glyceryl-3-phosphate
C21 H39 O7 P
ZQTAMPRZFOOEEP-KKFOGOCZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 86.980α = 90.00
b = 183.131β = 90.00
c = 127.498γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-08
    Type: Refinement description