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PDBsum entry 1obe
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Complex (immunoglobulin/peptide)
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PDB id
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1obe
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Contents |
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212 a.a.
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229 a.a.
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13 a.a.
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Theoretical model |
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PDB id:
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Complex (immunoglobulin/peptide)
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Title:
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Igg1 fab fragment 3d6 complexed with synthetic peptide, theoretical model
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Structure:
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Igg1 fab fragment 3d6. Chain: l, h. Gp41. Chain: p. Fragment: residues 605 - 617. Engineered: yes
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Source:
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Homo sapiens. Human. Synthetic: yes
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Authors:
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R.-D.Stigler,J.Schneider-Mergener
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Key ref:
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R.D.Stigler
et al.
(1995).
Interaction between a Fab fragment against gp41 of human immunodeficiency virus 1 and its peptide epitope: characterization using a peptide epitope library and molecular modeling.
Protein Eng,
8,
471-479.
PubMed id:
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Date:
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27-Jan-97
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Release date:
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15-May-97
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PROCHECK
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Headers
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References
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No UniProt id for this chain
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Protein Eng
8:471-479
(1995)
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PubMed id:
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Interaction between a Fab fragment against gp41 of human immunodeficiency virus 1 and its peptide epitope: characterization using a peptide epitope library and molecular modeling.
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R.D.Stigler,
F.Rüker,
D.Katinger,
G.Elliott,
W.Höhne,
P.Henklein,
J.X.Ho,
K.Keeling,
D.C.Carter,
E.Nugel.
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ABSTRACT
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The molecular interaction of the Fab fragment of the human monoclonal antibody
3D6, directed against the transmembrane protein gp41 of human immunodeficiency
virus (HIV) 1, with its peptide epitope is characterized by a panel of
overlapping peptides, a peptide epitope library and molecular modeling
techniques. The sequence CSGKLICTTAVPW, corresponding to amino acids 605-617 of
gp41, was identified as the best binding peptide (KD = 1 x 10(-8) mol/l). This
peptide served as a starting point to prepare a cellulose-bound peptide epitope
library in which each residue of the epitope is substituted by all L- and
D-amino acids, resulting in 494 epitope peptide variants which were subsequently
analyzed for binding 3D6. The library was synthesized to identify residues
critical for binding and to obtain information about the molecular environment
of the epitope peptide bound to 3D6. Both cysteine residues, as well as
isoleucine 6, threonine 8 and proline 12, of the epitope were highly sensitive
to substitution. Using the data obtained from the epitope characterization, as
well as a low-resolution electron density map of a 3D6 Fab-peptide complex, a
3-D model of the Fab-peptide complex was generated by molecular modeling. The
modeling experiments predict binding of the peptide, which is cyclized via the
two cysteine residues, to a pocket formed dominantly by the hypervariable loops
complementarity determining regions CDR3L, CDR2H and CDR3H.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Spenger,
R.Grabherr,
L.Töllner,
H.Katinger,
and
W.Ernst
(2002).
Altering the surface properties of baculovirus Autographa californica NPV by insertional mutagenesis of the envelope protein gp64.
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Eur J Biochem,
269,
4458-4467.
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A.P.Campbell,
W.Y.Wong,
R.T.Irvin,
and
B.D.Sykes
(2000).
Interaction of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pili strain PAK with a cross-reactive antibody: conformation of the bound peptide.
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Biochemistry,
39,
14847-14864.
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M.Valle,
M.Muñoz,
L.Kremer,
J.M.Valpuesta,
C.Martínez-A,
J.L.Carrascosa,
and
J.P.Albar
(1999).
Selection of antibody probes to correlate protein sequence domains with their structural distribution.
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Protein Sci,
8,
883-889.
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A.Kramer,
T.Keitel,
K.Winkler,
W.Stöcklein,
W.Höhne,
and
J.Schneider-Mergener
(1997).
Molecular basis for the binding promiscuity of an anti-p24 (HIV-1) monoclonal antibody.
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Cell,
91,
799-809.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
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Links
