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PDBsum entry 2bpx
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Hydrolase/hydrolase inhibitor
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PDB id
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2bpx
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Contents |
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* Residue conservation analysis
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Enzyme class 1:
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E.C.2.7.7.-
- ?????
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Enzyme class 2:
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E.C.2.7.7.49
- RNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 3:
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E.C.2.7.7.7
- DNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 4:
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E.C.3.1.-.-
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Enzyme class 5:
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E.C.3.1.13.2
- exoribonuclease H.
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Reaction:
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Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
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Enzyme class 6:
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E.C.3.1.26.13
- retroviral ribonuclease H.
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Enzyme class 7:
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E.C.3.4.23.16
- HIV-1 retropepsin.
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Reaction:
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Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Acta Crystallogr D Biol Crystallogr
54:1053-1060
(1998)
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PubMed id:
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Rapid X-ray diffraction analysis of HIV-1 protease-inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme.
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S.Munshi,
Z.Chen,
Y.Li,
D.B.Olsen,
M.E.Fraley,
R.W.Hungate,
L.C.Kuo.
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ABSTRACT
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The ability to replace an inhibitor bound to the HIV-1 protease in single
crystals with other potent inhibitors offers the possibility of investigating a
series of protease inhibitors rapidly and conveniently with the use of X-ray
crystallography. This approach affords a fast turnaround of structural
information for iterative rational drug designs and obviates the need for
studying the complex structures by co-crystallization. The replacement approach
has been successfully used with single crystals of the HIV-1 protease complexed
with a weak inhibitor. The structures of the complexes obtained by the
replacement method are similar to those determined by co-crystallization.
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Selected figure(s)
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Figure 3.
Fig. 3. (a)
Fo Fc
map contoured at 1.5a for
the complex of HIV1 protease and III. A
soaked crystal of the complex of the HIV
1 protease and I was soaked or 48 h in a
solution containing III, in absence of the
protease, prior to data collection. Map
was computed for data between 20.0 and
2.5 A resolution. The atomic model of III
(pink) built in to the density is super
imposed with the aomic model of I
(blue). (b) Fo Fc map contoured at
1.5a for the complex of HIV1 protease
and IV. The structure was determined
with a soaked crystal of the complex of
HIV1 protase and I in a solution
containing IV. Map was computed with
data between 22.0 and 2.8 A resolution.
The atomic model of IV (pink) built in to
the density is superimposed with the
atomic model of I (blue).
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1998,
54,
1053-1060)
copyright 1998.
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Figure was
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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M.Arenas,
M.C.Villaverde,
and
F.Sussman
(2009).
Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach.
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J Comput Chem,
30,
1229-1240.
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M.A.Dolan,
M.Keil,
and
D.S.Baker
(2008).
Comparison of composer and ORCHESTRAR.
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Proteins,
72,
1243-1258.
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A.Fernández,
R.Scott,
and
R.S.Berry
(2006).
Packing defects as selectivity switches for drug-based protein inhibitors.
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Proc Natl Acad Sci U S A,
103,
323-328.
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H.B.Thorsteinsdottir,
T.Schwede,
V.Zoete,
and
M.Meuwly
(2006).
How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding.
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Proteins,
65,
407-423.
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A.Fernández
(2005).
Incomplete protein packing as a selectivity filter in drug design.
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Structure,
13,
1829-1836.
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H.Petroková,
J.Dusková,
J.Dohnálek,
T.Skálová,
E.Vondrácková-Buchtelová,
M.Soucek,
J.Konvalinka,
J.Brynda,
M.Fábry,
J.Sedlácek,
and
J.Hasek
(2004).
Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV-1 protease inhibitors.
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Eur J Biochem,
271,
4451-4461.
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PDB code:
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A.Nayeem,
S.Krystek,
and
T.Stouch
(2003).
An assessment of protein-ligand binding site polarizability.
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Biopolymers,
70,
201-211.
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T.Gossas,
and
U.H.Danielson
(2003).
Analysis of the pH-dependencies of the association and dissociation kinetics of HIV-1 protease inhibitors.
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J Mol Recognit,
16,
203-212.
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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
