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PDBsum entry 2k5x
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Immune system/hydrolase
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PDB id
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2k5x
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Contents |
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* Residue conservation analysis
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J Am Chem Soc
130:15990-15996
(2008)
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PubMed id:
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Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex.
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R.W.Montalvao,
A.Cavalli,
X.Salvatella,
T.L.Blundell,
M.Vendruscolo.
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ABSTRACT
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Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful
techniques for determining the structures and the dynamics of proteins. The
high-resolution determination of the structures of protein-protein complexes,
however, is still a challenging problem for this approach, since it can normally
provide only a limited amount of structural information at protein-protein
interfaces. We present here the determination using NMR chemical shifts of the
structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial
toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order
to achieve this result, we introduce the CamDock method, which combines a
flexible docking procedure with a refinement that exploits the structural
information provided by chemical shifts. The results that we report thus
indicate that chemical shifts can be used as structural restraints for the
determination of the conformations of protein complexes that are difficult to
obtain by more standard NMR approaches.
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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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N.Rawat,
and
P.Biswas
(2011).
Shape, flexibility and packing of proteins and nucleic acids in complexes.
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Phys Chem Chem Phys,
13,
9632-9643.
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J.Abi-Ghanem,
B.Heddi,
N.Foloppe,
and
B.Hartmann
(2010).
DNA structures from phosphate chemical shifts.
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Nucleic Acids Res,
38,
e18.
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J.H.Tomlinson,
V.L.Green,
P.J.Baker,
and
M.P.Williamson
(2010).
Structural origins of pH-dependent chemical shifts in the B1 domain of protein G.
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Proteins,
78,
3000-3016.
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PDB code:
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P.Robustelli,
K.Kohlhoff,
A.Cavalli,
and
M.Vendruscolo
(2010).
Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins.
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Structure,
18,
923-933.
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S.J.de Vries,
A.S.Melquiond,
P.L.Kastritis,
E.Karaca,
A.Bordogna,
M.van Dijk,
J.P.Rodrigues,
and
A.M.Bonvin
(2010).
Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.
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Proteins,
78,
3242-3249.
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R.Das,
I.André,
Y.Shen,
Y.Wu,
A.Lemak,
S.Bansal,
C.H.Arrowsmith,
T.Szyperski,
and
D.Baker
(2009).
Simultaneous prediction of protein folding and docking at high resolution.
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Proc Natl Acad Sci U S A,
106,
18978-18983.
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P.Robustelli,
A.Cavalli,
and
M.Vendruscolo
(2008).
Determination of protein structures in the solid state from NMR chemical shifts.
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Structure,
16,
1764-1769.
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PDB code:
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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
