1NLD

FAB FRAGMENT OF A NEUTRALIZING ANTIBODY DIRECTED AGAINST AN EPITOPE OF GP41 FROM HIV-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Fab fragment from a neutralizing monoclonal antibody directed against an epitope of gp41 from HIV-1.

Davies, C.Beauchamp, J.C.Emery, D.Rawas, A.Muirhead, H.

(1997) Acta Crystallogr.,Sect.D 53: 186-194

  • DOI: 10.1107/S0907444996012048

  • PubMed Abstract: 
  • The structure of a Fab fragment of a monoclonal antibody (1583) that neutralizes a broad range of HIV-1 isolates has been solved by X-ray crystallography. This antibody is directed against a poliovirus/HIV-I chimaera which presents a conserved epitop ...

    The structure of a Fab fragment of a monoclonal antibody (1583) that neutralizes a broad range of HIV-1 isolates has been solved by X-ray crystallography. This antibody is directed against a poliovirus/HIV-I chimaera which presents a conserved epitope of the envelope protein gp41. Crystals of 1583 were obtained in the space group P2(1)2(1)2(1) and the structure solved by molecular replacement. The model has been refined against all data in the range 10-2.9 A to a final crystallographic R factor of 0.198. The antigen-binding site features a well defined groove, typical of antibodies that bind to small antigens, created in part by a relatively short CDR H3. The variable regions of 1583 were sequenced and, given the hydrophilic nature of the epitope, revealed a surprising lack of charged residues in the CDR's. However, the antigen-binding cleft is indeed very polar, due in part to the presence of two charged residues that emanate from outside the recognized CDR's.


    Related Citations: 
    • An Engineered Poliovirus Chimaera Elicits Broadly Reactive HIV-1 Neutralizing Antibodies
      Evans, D.J.,Mckeating, J.,Meredith, J.M.,Burke, K.L.,Katrak, K.,John, A.,Ferguson, M.,Minor, P.D.,Weiss, R.A.,Almond, J.W.
      (1989) Nature 339: 385


    Organizational Affiliation

    Department of Biochemistry and Molecular Recognition Centre, University of Bristol, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAB1583
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB1583
H
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.150α = 90.00
b = 82.550β = 90.00
c = 131.000γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
XENGENdata collection
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance