1N4X | pdb_00001n4x

Structure of scFv 1696 at acidic pH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Structure of a single-chain Fv fragment of an antibody that inhibits the HIV-1 and HIV-2 proteases.

Lescar, J., Brynda, J., Fabry, M., Horejsi, M., Rezacova, P., Sedlacek, J., Bentley, G.A.

(2003) Acta Crystallogr D Biol Crystallogr 59: 955-957

  • DOI: https://doi.org/10.1107/s0907444903003597
  • Primary Citation of Related Structures:  
    1N4X

  • PubMed Abstract: 

    The monoclonal antibody 1696, which was raised against the HIV-1 protease, inhibits the catalytic activity of the enzyme from both the HIV-1 and HIV-2 strains. The antibody cross-reacts with peptides containing the N-terminus of the enzyme, which is highly conserved between these strains. The crystal structure of a single-chain Fv fragment of 1696 (scFv-1696) in the non-complexed form, solved at 1.7 A resolution, is compared with the previously reported non-complexed Fab-1696 and antigen-bound scFv-1696 structures. Large conformational changes in the third hypervariable region of the heavy chain and differences in relative orientation of the variable domains are observed between the different structures.

    • Organizational Affiliation: 
    • European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble, France.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
immunoglobulin kappa chain variable regionA [auth L],
C [auth M]		113Mus musculusMutation(s): 0 
UniProt
Find proteins for P01631 (Mus musculus)
Explore P01631 
Go to UniProtKB:  P01631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01631
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
immunoglobulin heavy chain variable regionB [auth H],
D [auth I]		120Mus musculusMutation(s): 0 
UniProt
Find proteins for Q921A6 (Mus musculus)
Explore Q921A6 
Go to UniProtKB:  Q921A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ921A6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.93α = 90
b = 61.21β = 90
c = 57.3γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-11-13
    Changes: Data collection, Structure summary