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* Residue conservation analysis
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Nat Struct Biol
2:466-471
(1995)
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PubMed id:
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The x-ray structure of an anti-tumour antibody in complex with antigen.
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P.D.Jeffrey,
J.Bajorath,
C.Y.Chang,
D.Yelton,
I.Hellström,
K.E.Hellström,
S.Sheriff.
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ABSTRACT
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The crystal structures of the murine BR96 Fab and its human chimera have been
determined in complex with the nonoate methyl ester derivative of Lewis Y (nLey)
at 2.8 A and 2.5 A resolution, respectively. BR96 binds the carbohydrate in a
large pocket which is formed by residues of all CDR loops except L2. The binding
of the carbohydrate is mediated predominantly by aromatic residues in BR96.
Analysis of the structure suggests that BR96 is capable of recognizing a
structure larger than the Le(y) tetrasaccharide, providing a possible
explanation for its high tumour selectivity. The structure provides a rationale
for mutagenesis experiments that have resulted in BR96 CDR loop mutants with
increased affinity for nLey and/or tumour cells.
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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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C.L.Brooks,
R.J.Blackler,
G.Sixta,
P.Kosma,
S.Müller-Loennies,
L.Brade,
T.Hirama,
C.R.MacKenzie,
H.Brade,
and
S.V.Evans
(2010).
The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen.
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Glycobiology,
20,
138-147.
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PDB codes:
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C.L.Brooks,
S.Müller-Loennies,
S.N.Borisova,
L.Brade,
P.Kosma,
T.Hirama,
C.R.Mackenzie,
H.Brade,
and
S.V.Evans
(2010).
Antibodies raised against chlamydial lipopolysaccharide antigens reveal convergence in germline gene usage and differential epitope recognition.
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Biochemistry,
49,
570-581.
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PDB codes:
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S.Tapryal,
Y.Pal Khasa,
and
K.J.Mukherjee
(2010).
Single chain Fv fragment specific for human GM-CSF: selection and expression using a bacterial expression library.
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Biotechnol J,
5,
1078-1089.
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D.C.de Geus,
A.M.van Roon,
E.A.Thomassen,
C.H.Hokke,
A.M.Deelder,
and
J.P.Abrahams
(2009).
Characterization of a diagnostic Fab fragment binding trimeric Lewis X.
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Proteins,
76,
439-447.
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PDB code:
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L.Krishnan,
G.Sahni,
K.J.Kaur,
and
D.M.Salunke
(2008).
Role of antibody paratope conformational flexibility in the manifestation of molecular mimicry.
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Biophys J,
94,
1367-1376.
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PDB code:
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J.Milland,
E.Yuriev,
P.X.Xing,
I.F.McKenzie,
P.A.Ramsland,
and
M.S.Sandrin
(2007).
Carbohydrate residues downstream of the terminal Galalpha(1,3)Gal epitope modulate the specificity of xenoreactive antibodies.
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Immunol Cell Biol,
85,
623-632.
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N.Monnier,
K.Higo-Moriguchi,
Z.Y.Sun,
B.V.Prasad,
K.Taniguchi,
and
P.R.Dormitzer
(2006).
High-resolution molecular and antigen structure of the VP8* core of a sialic acid-independent human rotavirus strain.
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J Virol,
80,
1513-1523.
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PDB code:
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E.Yuriev,
W.Farrugia,
A.M.Scott,
and
P.A.Ramsland
(2005).
Three-dimensional structures of carbohydrate determinants of Lewis system antigens: implications for effective antibody targeting of cancer.
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Immunol Cell Biol,
83,
709-717.
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U.Krengel,
L.L.Olsson,
C.Martínez,
A.Talavera,
G.Rojas,
E.Mier,
J.Angström,
and
E.Moreno
(2004).
Structure and molecular interactions of a unique antitumor antibody specific for N-glycolyl GM3.
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J Biol Chem,
279,
5597-5603.
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PDB code:
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H.P.Nguyen,
N.O.Seto,
C.R.MacKenzie,
L.Brade,
P.Kosma,
H.Brade,
and
S.V.Evans
(2003).
Germline antibody recognition of distinct carbohydrate epitopes.
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Nat Struct Biol,
10,
1019-1025.
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PDB codes:
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N.K.Vyas,
M.N.Vyas,
M.C.Chervenak,
D.R.Bundle,
B.M.Pinto,
and
F.A.Quiocho
(2003).
Structural basis of peptide-carbohydrate mimicry in an antibody-combining site.
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Proc Natl Acad Sci U S A,
100,
15023-15028.
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PDB code:
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S.Muller-Loennies,
L.Brade,
C.R.MacKenzie,
F.E.Di Padova,
and
H.Brade
(2003).
Identification of a cross-reactive epitope widely present in lipopolysaccharide from enterobacteria and recognized by the cross-protective monoclonal antibody WN1 222-5.
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J Biol Chem,
278,
25618-25627.
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M.Nitz,
C.C.Ling,
A.Otter,
J.E.Cutler,
and
D.R.Bundle
(2002).
The unique solution structure and immunochemistry of the Candida albicans beta -1,2-mannopyranan cell wall antigens.
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J Biol Chem,
277,
3440-3446.
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E.L.Nason,
J.D.Wetzel,
S.K.Mukherjee,
E.S.Barton,
B.V.Prasad,
and
T.S.Dermody
(2001).
A monoclonal antibody specific for reovirus outer-capsid protein sigma3 inhibits sigma1-mediated hemagglutination by steric hindrance.
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J Virol,
75,
6625-6634.
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G.Cunto-Amesty,
P.Luo,
B.Monzavi-Karbassi,
and
T.Kieber-Emmons
(2001).
Exploiting molecular mimicry: defining rules of the game.
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Int Rev Immunol,
20,
157-180.
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S.Villeneuve,
H.Souchon,
M.M.Riottot,
J.C.Mazie,
P.Lei,
C.P.Glaudemans,
P.Kovác,
J.M.Fournier,
and
P.M.Alzari
(2000).
Crystal structure of an anti-carbohydrate antibody directed against Vibrio cholerae O1 in complex with antigen: molecular basis for serotype specificity.
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Proc Natl Acad Sci U S A,
97,
8433-8438.
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PDB codes:
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C.A.Bush,
M.Martin-Pastor,
and
A.Imberty
(1999).
Structure and conformation of complex carbohydrates of glycoproteins, glycolipids, and bacterial polysaccharides.
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Annu Rev Biophys Biomol Struct,
28,
269-293.
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S.Odani,
Y.Komori,
and
F.Gejyo
(1999).
Structural analysis of the amyloidogenic kappa Bence Jones protein (FUR).
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Amyloid,
6,
77-88.
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Z.C.Fan,
L.Shan,
B.Z.Goldsteen,
L.W.Guddat,
A.Thakur,
N.F.Landolfi,
M.S.Co,
M.Vasquez,
C.Queen,
P.A.Ramsland,
and
A.B.Edmundson
(1999).
Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an anti-gamma-interferon antibody.
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J Mol Recognit,
12,
19-32.
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PDB codes:
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A.Babino,
O.Pritsch,
P.Oppezzo,
R.Du Pasquier,
A.Roseto,
E.Osinaga,
and
P.M.Alzari
(1997).
Molecular cloning of a monoclonal anti-tumor antibody specific for the Tn antigen and expression of an active single-chain Fv fragment.
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Hybridoma,
16,
317-324.
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C.H.Trinh,
S.D.Hemmington,
M.E.Verhoeyen,
and
S.E.Phillips
(1997).
Antibody fragment Fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity.
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Structure,
5,
937-948.
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PDB codes:
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M.J.Rosok,
D.E.Yelton,
L.J.Harris,
J.Bajorath,
K.E.Hellström,
I.Hellström,
G.A.Cruz,
K.Kristensson,
H.Lin,
W.D.Huse,
and
S.M.Glaser
(1996).
A combinatorial library strategy for the rapid humanization of anticarcinoma BR96 Fab.
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J Biol Chem,
271,
22611-22618.
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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.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
