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PDBsum entry 2cio
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Hydrolase/inhibitor
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PDB id
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2cio
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References listed in PDB file
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Key reference
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Title
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High-Resolution complex of papain with remnants of a cysteine protease inhibitor derived from trypanosoma brucei.
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Authors
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M.S.Alphey,
W.N.Hunter.
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Ref.
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Acta Crystallograph Sect F Struct Biol Cryst Commun, 2006,
62,
504-508.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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Attempts to cocrystallize the cysteine protease papain derived from the latex of
Carica papaya with an inhibitor of cysteine proteases (ICP) from Trypanosoma
brucei were unsuccessful. However, crystals of papain that diffracted to higher
resolution, 1.5 A, than other crystals of this archetypal cysteine protease were
obtained, so the analysis was continued. Surprisingly, the substrate-binding
cleft was occupied by two short peptide fragments which have been assigned as
remnants of ICP. Comparisons reveal that these peptides bind in the active site
in a manner similar to that of the human cysteine protease inhibitor stefin B
when it is complexed to papain. The assignment of the fragment sequences is
consistent with the specificity of the protease.
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Figure 1.
Figure 1 An omit difference electron-density map for Glu118
calculated with coefficients (F[o] - F[c]) and contoured at 3
 (magenta)
revealing the hydrogen-bonding (yellow dashed lines) pattern
that defines the side-chain properties. F[o] and F[c] represent
the observed and calculated structure factors, respectively. The
refined model is shown in sticks with O atoms in red, N atoms in
blue and C atoms in white. All figures were prepared using PyMOL
(DeLano, 2002[DeLano, W. L. (2002). The PyMOL Molecular Graphics
System. DeLano Scientific, San Carlos, CA, USA.]).
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Figure 3.
Figure 3 Selected active-site details. Putative
hydrogen-bonding interactions (green dashed lines) between
papain (sticks coloured C black, O red, N blue, S yellow) and
the peptide fragments derived from TbICP (sticks coloured C
orange, O red, N blue) are depicted. The OD1, OD2 and OD3 atoms
associated with the sulfonic acid group of Cys25 are labelled 1,
2 and 3, respectively; water molecules are shown as red spheres
and labelled W.
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The above figures are
reprinted
from an Open Access publication published by the IUCr:
Acta Crystallograph Sect F Struct Biol Cryst Commun
(2006,
62,
504-508)
copyright 2006.
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