2B2X

VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design

Clark, L.A., Boriack-Sjodin, P.A., Eldredge, J., Fitch, C., Friedman, B., Hanf, K.J., Jarpe, M., Liparoto, S.F., Li, Y., Lugovskoy, A., Miller, S., Rushe, M., Sherman, W., Simon, K., Van Vlijmen, H.

(2006) Protein Sci. 15: 949-960

  • DOI: 10.1110/ps.052030506

  • PubMed Abstract: 

    • Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize ...

    Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 A. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies.

    Organizational Affiliation: 

    Biogen Idec, Inc., Cambridge, Massachusetts 02142, USA. louie@alumni.northwestern.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-1
A, B
223Rattus norvegicusMutation(s): 4 
Gene Names: Itga1
Find proteins for P18614 (Rattus norvegicus)
Go to UniProtKB:  P18614
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody AQC2 Fab
H, I
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antibody AQC2 Fab
L, M
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.238 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.120α = 90.00
b = 43.680β = 104.10
c = 153.880γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNXrefinement
CNSrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-11
    Type: Refinement description