2B2X

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.5 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
  • Primary Citation of Related Structures:  
    2B2X

  • 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 the binding affinity of an antibody fragment to the I-domain of the integrin VLA1 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin alpha-1A,
D [auth B]		223Rattus norvegicusMutation(s): 4 
Gene Names: Itga1
UniProt
Find proteins for P18614 (Rattus norvegicus)
Explore P18614 
Go to UniProtKB:  P18614
Entity Groups  
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UniProt GroupP18614
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody AQC2 FabB [auth H],
E [auth I]		226Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody AQC2 FabC [auth L],
F [auth M]		213Mus musculusMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.12α = 90
b = 43.68β = 104.1
c = 153.88γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations