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Contents |
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212 a.a.
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214 a.a.
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129 a.a.
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* Residue conservation analysis
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PDB id:
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Immunoglobulin/hydrolase(o-glycosyl)
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Title:
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Structure of an antibody-lysozyme complex: effect of a conservative mutation
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Structure:
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Igg1 hyhel-5 fab (light chain). Chain: l. Engineered: yes. Igg1 hyhel-5 fab (heavy chain). Chain: h. Engineered: yes. Hen egg white lysozyme. Chain: y. Engineered: yes.
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Gallus gallus. Chicken. Organism_taxid: 9031. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
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Biol. unit:
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Trimer (from
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Resolution:
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2.65Å
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R-factor:
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not given
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Authors:
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S.Chacko,D.R.Davies
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Key ref:
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S.Chacko
et al.
(1995).
Structure of an antibody-lysozyme complex unexpected effect of conservative mutation.
J Mol Biol,
245,
261-274.
PubMed id:
DOI:
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Date:
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03-Feb-94
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Release date:
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31-May-94
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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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Enzyme class:
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Chain Y:
E.C.3.2.1.17
- lysozyme.
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Reaction:
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Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
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DOI no:
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J Mol Biol
245:261-274
(1995)
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PubMed id:
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Structure of an antibody-lysozyme complex unexpected effect of conservative mutation.
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S.Chacko,
E.Silverton,
L.Kam-Morgan,
S.Smith-Gill,
G.Cohen,
D.Davies.
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ABSTRACT
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The structure of the complex between the Fab HyHEL-5 and chicken lysozyme
revealed a large interface region containing 23 lysozyme and 28 Fab residues.
Arg68 of the lysozyme is centrally placed in this interface and theoretical
studies together with binding assays of this Fab to different avian lysozymes
have previously shown that this arginine residue is an important contributor to
the binding. The Arg68-->Lys mutant binds 10(3) times less well to the
HyHEL-5 Fab. We have examined the refined crystal structure of the complex of
this mutant lysozyme with the Fab. No global changes occur, but there is an
introduction of a new water molecule into the interface that mediates the
hydrogen bonding interactions between the lysine and residues on the Fab. These
data are compared with the effects of similar changes on the inhibition of
serine proteases such as trypsin where the energetic effects of this
substitution are small.
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Selected figure(s)
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Figure 8.
Figure 8. Hydrogen bonding interactions around the 68(Y) pocket in the native and mutant structures.
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Figure 9.
Figure 9. Hydrogen bonding in the active site of the native and mutant BPTI--trypsin complexes.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1995,
245,
261-274)
copyright 1995.
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Figures were
selected
by an automated process.
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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.K.Füzéry,
J.J.Oh,
D.T.Ta,
L.E.Vickery,
and
J.L.Markley
(2011).
Three hydrophobic amino acids in Escherichia coli HscB make the greatest contribution to the stability of the HscB-IscU complex.
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BMC Biochem,
12,
3.
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Z.Li,
and
T.Lazaridis
(2007).
Water at biomolecular binding interfaces.
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Phys Chem Chem Phys,
9,
573-581.
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R.J.Duquesnoy
(2006).
A structurally based approach to determine HLA compatibility at the humoral immune level.
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Hum Immunol,
67,
847-862.
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F.Rodier,
R.P.Bahadur,
P.Chakrabarti,
and
J.Janin
(2005).
Hydration of protein-protein interfaces.
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Proteins,
60,
36-45.
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G.H.Cohen,
E.W.Silverton,
E.A.Padlan,
F.Dyda,
J.A.Wibbenmeyer,
R.C.Willson,
and
D.R.Davies
(2005).
Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.
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Acta Crystallogr D Biol Crystallogr,
61,
628-633.
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PDB code:
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M.Becker,
J.Bunikis,
B.D.Lade,
J.J.Dunn,
A.G.Barbour,
and
C.L.Lawson
(2005).
Structural investigation of Borrelia burgdorferi OspB, a bactericidal Fab target.
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J Biol Chem,
280,
17363-17370.
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PDB codes:
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A.Yokota,
K.Tsumoto,
M.Shiroishi,
H.Kondo,
and
I.Kumagai
(2003).
The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction.
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J Biol Chem,
278,
5410-5418.
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PDB codes:
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J.G.Luz,
M.Huang,
K.C.Garcia,
M.G.Rudolph,
V.Apostolopoulos,
L.Teyton,
and
I.A.Wilson
(2002).
Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.
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J Exp Med,
195,
1175-1186.
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PDB codes:
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K.Sakurai,
and
Y.Goto
(2002).
Manipulating monomer-dimer equilibrium of bovine Beta -lactoglobulin by amino acid substitution.
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J Biol Chem,
277,
25735-25740.
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M.G.Rudolph,
J.A.Speir,
A.Brunmark,
N.Mattsson,
M.R.Jackson,
P.A.Peterson,
L.Teyton,
and
I.A.Wilson
(2001).
The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity.
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Immunity,
14,
231-242.
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PDB codes:
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D.Fleury,
R.S.Daniels,
J.J.Skehel,
M.Knossow,
and
T.Bizebard
(2000).
Structural evidence for recognition of a single epitope by two distinct antibodies.
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Proteins,
40,
572-578.
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PDB code:
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J.A.Wibbenmeyer,
P.Schuck,
S.J.Smith-Gill,
and
R.C.Willson
(1999).
Salt links dominate affinity of antibody HyHEL-5 for lysozyme through enthalpic contributions.
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J Biol Chem,
274,
26838-26842.
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J.Janin
(1999).
Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition.
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Structure,
7,
R277-R279.
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R.Helland,
G.I.Berglund,
J.Otlewski,
W.Apostoluk,
O.A.Andersen,
N.P.Willassen,
and
A.O.Smalås
(1999).
High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes.
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Acta Crystallogr D Biol Crystallogr,
55,
139-148.
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PDB codes:
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B.Vallone,
A.E.Miele,
P.Vecchini,
E.Chiancone,
and
M.Brunori
(1998).
Free energy of burying hydrophobic residues in the interface between protein subunits.
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Proc Natl Acad Sci U S A,
95,
6103-6107.
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T.L.McInerney,
W.El Ahmar,
B.E.Kemp,
and
P.Poumbourios
(1998).
Mutation-directed chemical cross-linking of human immunodeficiency virus type 1 gp41 oligomers.
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J Virol,
72,
1523-1533.
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W.Dall'Acqua,
E.R.Goldman,
W.Lin,
C.Teng,
D.Tsuchiya,
H.Li,
X.Ysern,
B.C.Braden,
Y.Li,
S.J.Smith-Gill,
and
R.A.Mariuzza
(1998).
A mutational analysis of binding interactions in an antigen-antibody protein-protein complex.
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Biochemistry,
37,
7981-7991.
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PDB code:
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K.A.Xavier,
K.A.Shick,
S.J.Smith-Gil,
and
R.C.Willson
(1997).
Involvement of water molecules in the association of monoclonal antibody HyHEL-5 with bobwhite quail lysozyme.
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Biophys J,
73,
2116-2125.
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B.A.Fields,
F.A.Goldbaum,
W.Dall'Acqua,
E.L.Malchiodi,
A.Cauerhff,
F.P.Schwarz,
X.Ysern,
R.J.Poljak,
and
R.A.Mariuzza
(1996).
Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.
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Biochemistry,
35,
15494-15503.
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PDB codes:
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D.R.Davies,
and
G.H.Cohen
(1996).
Interactions of protein antigens with antibodies.
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Proc Natl Acad Sci U S A,
93,
7.
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P.Bork,
A.K.Downing,
B.Kieffer,
and
I.D.Campbell
(1996).
Structure and distribution of modules in extracellular proteins.
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Q Rev Biophys,
29,
119-167.
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T.Brocker,
M.Riedinger,
and
K.Karjalainen
(1996).
Redirecting the complete T cell receptor/CD3 signaling machinery towards native antigen via modified T cell receptor.
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Eur J Immunol,
26,
1770-1774.
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A.Shaw,
P.A.Fortes,
C.D.Stout,
and
V.D.Vacquier
(1995).
Crystal structure and subunit dynamics of the abalone sperm lysin dimer: egg envelopes dissociate dimers, the monomer is the active species.
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J Cell Biol,
130,
1117-1125.
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PDB code:
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I.M.Tomlinson,
J.P.Cox,
E.Gherardi,
A.M.Lesk,
and
C.Chothia
(1995).
The structural repertoire of the human V kappa domain.
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EMBO J,
14,
4628-4638.
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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
code is
shown on the right.
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Links
