1F90

FAB FRAGMENT OF MONOCLONAL ANTIBODY (LNKB-2) AGAINST HUMAN INTERLEUKIN-2 IN COMPLEX WITH ANTIGENIC PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide.

Afonin, P.V.Fokin, A.V.Tsygannik, I.N.Mikhailova, I.Y.Onoprienko, L.V.Mikhaleva, I.I.Ivanov, V.T.Mareeva, T.Y.Nesmeyanov, V.A.Li, N.Pangborn, W.A.Duax, W.L.Pletnev, V.Z.

(2001) Protein Sci 10: 1514-1521

  • DOI: 10.1110/ps.3101
  • Primary Citation of Related Structures:  
    1F90

  • PubMed Abstract: 
  • The three-dimensional structure of the Fab fragment of a monoclonal antibody (LNKB-2) to human interleukin-2 (IL-2) complexed with a synthetic antigenic nonapeptide, Ac-Lys-Pro-Leu-Glu-Glu-Val-Leu-Asn-Leu-OMe, has been determined at 3.0 A resolution. In the structure, four out of the six hypervariable loops of the Fab (complementarity determining regions [CDRs] L1, H1, H2, and H3) are involved in peptide association through hydrogen bonding, salt bridge formation, and hydrophobic interactions ...

    The three-dimensional structure of the Fab fragment of a monoclonal antibody (LNKB-2) to human interleukin-2 (IL-2) complexed with a synthetic antigenic nonapeptide, Ac-Lys-Pro-Leu-Glu-Glu-Val-Leu-Asn-Leu-OMe, has been determined at 3.0 A resolution. In the structure, four out of the six hypervariable loops of the Fab (complementarity determining regions [CDRs] L1, H1, H2, and H3) are involved in peptide association through hydrogen bonding, salt bridge formation, and hydrophobic interactions. The Tyr residues in the Fab antigen binding site play a major role in antigen-antibody recognition. The structures of the complexed and uncomplexed Fab were compared. In the antigen binding site the CDR-L1 loop of the antibody shows the largest structural changes upon peptide binding. The peptide adopts a mostly alpha-helical conformation similar to that in the epitope fragment 64-72 of the IL-2 antigen. The side chains of residues Leu 66, Val 69, and Leu 70, which are shielded internally in the IL-2 structure, are involved in interactions with the Fab in the complex studied. This indicates that antibody-antigen complexation involves a significant rearrangement of the epitope-containing region of the IL-2 with retention of the alpha-helical character of the epitope fragment.


    Related Citations: 
    • THREE-DIMENSIONAL STRUCTURE OF ANTIGEN BINDING FRAGMENT OF MONOCLONAL ANTIBODY AGAINST HUMAN INTERLEUKIN-2 IN TWO CRYSTAL FORMS AT 2.2 AND 2.9 A RESOLUTION.
      Fokin, A.V., Afonin, P.V., Mikhailova, I.Y., Tsygannik, I.N., Mareeva, T.Y., Nesmeyanov, V.A., Pangborn, W., Lee, N., Duax, W., Sijak, E., Pletnev, V.Z.
      (2000) Bioorg Khim 26: 571

    Organizational Affiliation

    Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117871 Moscow, Russia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENT OF MONOCLONAL ANTIBODYA [auth L]219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENT OF MONOCLONAL ANTIBODYB [auth H]220Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIGENIC NONAPEPTIDEC [auth E]9N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.83α = 90
b = 72.76β = 106.98
c = 72.15γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection