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* Residue conservation analysis
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PDB id:
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Hydrolase/hydrolase inhibitor
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Title:
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Crystal and molecular structures of the complex of alpha- Chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 angstroms resolution
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Structure:
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Alpha-chymotrypsin a. Chain: e. Alpha-chymotrypsin a. Chain: f. Alpha-chymotrypsin a. Chain: g. Turkey ovomucoid third domain (omtky3). Chain: i
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Source:
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Bos taurus. Cattle. Organism_taxid: 9913. Meleagris gallopavo. Turkey. Organism_taxid: 9103
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Biol. unit:
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Tetramer (from
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Resolution:
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Authors:
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M.Fujinaga,A.R.Sielecki,R.J.Read,W.Ardelt,M.Laskowskijunior, M.N.G.James
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Key ref:
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M.Fujinaga
et al.
(1987).
Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution.
J Mol Biol,
195,
397-418.
PubMed id:
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Date:
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04-Mar-88
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Release date:
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16-Jul-88
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PROCHECK
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Headers
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References
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P00766
(CTRA_BOVIN) -
Chymotrypsinogen A from Bos taurus
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Seq:
Struc:
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245 a.a.
131 a.a.
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Enzyme class:
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Chains F, G:
E.C.3.4.21.1
- chymotrypsin.
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Reaction:
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Preferential cleavage: Tyr-|-Xaa, Trp-|-Xaa, Phe-|-Xaa, Leu-|-Xaa.
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J Mol Biol
195:397-418
(1987)
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PubMed id:
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Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution.
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M.Fujinaga,
A.R.Sielecki,
R.J.Read,
W.Ardelt,
M.Laskowski,
M.N.James.
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ABSTRACT
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The molecular structure of the complex between bovine pancreatic
alpha-chymotrypsin (EC 3.4.4.5) and the third domain of the Kazal-type ovomucoid
from Turkey (OMTKY3) has been determined crystallographically by the molecular
replacement method. Restrained-parameter least-squares refinement of the
molecular model of the complex has led to a conventional agreement factor R of
0.168 for the 19,466 reflections in the 1.8 A (1 A = 0.1 nm) resolution shell [I
greater than or equal to sigma (I)]. The reactive site loop of OMTKY3, from
Lys13I to Arg21I (I indicates inhibitor), is highly complementary to the surface
of alpha-chymotrypsin in the complex. A total of 13 residues on the inhibitor
make 113 contacts of less than 4.0 A with 21 residues of the enzyme. A short
contact (2.95 A) from O gamma of Ser195 to the carbonyl-carbon atom of the
scissile bond between Leu18I and Glu19I is present; in spite of it, this peptide
remains planar and undistorted. Analysis of the interactions of the inhibitor
with chymotrypsin explains the enhanced specificity that chymotrypsin has for
P'3 arginine residues. There is a water-mediated ion pair between the
guanidinium group on this residue and the carboxylate of Asp64. Comparison of
the structure of the alpha-chymotrypsin portion of this complex with the several
structures of alpha and gamma-chymotrypsin in the uncomplexed form shows a high
degree of structural equivalence (root-mean-square deviation of the 234 common
alpha-carbon atoms averages 0.38 A). Significant differences occur mainly in two
regions Lys36 to Phe39 and Ser75 to Lys79. Among the 21 residues that are in
contact with the ovomucoid domain, only Phe39 and Tyr146 change their
conformations significantly as a result of forming the complex. Comparison of
the structure of the OMTKY3 domain in this complex to that of the same inhibitor
bound to a serine proteinase from Streptomyces griseus (SGPB) shows a central
core of 44 amino acids (the central alpha-helix and flanking small 3-stranded
beta-sheet) that have alpha-carbon atoms fitting to within 1.0 A
(root-mean-square deviation of 0.45 A) whereas the residues of the reactive-site
loop differ in position by up to 1.9 A (C alpha of Leu18I). The ovomucoid domain
has a built-in conformational flexibility that allows it to adapt to the active
sites of different enzymes. A comparison of the SGPB and alpha-chymotrypsin
molecules is made and the water molecules bound at the inhibitor-enzyme
interface in both complexes are analysed for similarities and differences.
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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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K.M.Dunse,
Q.Kaas,
R.F.Guarino,
P.A.Barton,
D.J.Craik,
and
M.A.Anderson
(2010).
Molecular basis for the resistance of an insect chymotrypsin to a potato type II proteinase inhibitor.
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Proc Natl Acad Sci U S A,
107,
15016-15021.
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N.M.Ng,
R.N.Pike,
and
S.E.Boyd
(2009).
Subsite cooperativity in protease specificity.
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Biol Chem,
390,
401-407.
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F.H.Schumann,
H.Riepl,
T.Maurer,
W.Gronwald,
K.P.Neidig,
and
H.R.Kalbitzer
(2007).
Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions.
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J Biomol NMR,
39,
275-289.
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J.Janin,
F.Rodier,
P.Chakrabarti,
and
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(2007).
Macromolecular recognition in the Protein Data Bank.
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Acta Crystallogr D Biol Crystallogr,
63,
1-8.
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M.I.Hassan,
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and
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(2007).
Structural model of human PSA: a target for prostate cancer therapy.
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Chem Biol Drug Des,
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M.J.Lemieux,
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and
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(2007).
The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis.
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Proc Natl Acad Sci U S A,
104,
750-754.
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PDB code:
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M.Almlöf,
J.Aqvist,
A.O.Smalås,
and
B.O.Brandsdal
(2006).
Probing the effect of point mutations at protein-protein interfaces with free energy calculations.
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Biophys J,
90,
433-442.
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Z.Yi,
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M.A.Qasim,
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M.C.Laskowski,
C.Bailey-Kellogg,
and
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(2006).
Functional evolution within a protein superfamily.
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Proteins,
63,
697-708.
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D.Segal,
and
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(2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
|
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Proteins,
59,
580-591.
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J.T.Maynes,
M.M.Cherney,
M.A.Qasim,
M.Laskowski,
and
M.N.James
(2005).
Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.
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Acta Crystallogr D Biol Crystallogr,
61,
580-588.
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PDB code:
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M.Taniguchi,
K.Kamei,
K.Kanaori,
T.Koyama,
T.Yasui,
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and
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(2005).
Relationship between temporary inhibition and structure of disulfide-linkage analogs of marinostatin, a natural ester-linked protein protease inhibitor.
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J Pept Res,
66,
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T.Jabeen,
S.Sharma,
I.Roy,
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S.Dey,
M.Perbandt,
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A.Srinivasan,
and
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(2005).
Detection of native peptides as potent inhibitors of enzymes. Crystal structure of the complex formed between treated bovine alpha-chymotrypsin and an autocatalytically produced fragment, IIe-Val-Asn-Gly-Glu-Glu-Ala-Val-Pro-Gly-Ser-Trp-Pro-Trp, at 2.2 angstroms resolution.
|
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FEBS J,
272,
562-572.
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PDB code:
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Z.Zhu,
Z.Liang,
T.Zhang,
Z.Zhu,
W.Xu,
M.Teng,
and
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(2005).
Crystal structures and amidolytic activities of two glycosylated snake venom serine proteinases.
|
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J Biol Chem,
280,
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PDB codes:
|
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A.Berchanski,
B.Shapira,
and
M.Eisenstein
(2004).
Hydrophobic complementarity in protein-protein docking.
|
| |
Proteins,
56,
130-142.
|
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|
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|
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Y.P.Pang
(2004).
Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding.
|
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Proteins,
57,
747-757.
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PDB codes:
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I.H.Barrette-Ng,
K.K.Ng,
M.M.Cherney,
G.Pearce,
U.Ghani,
C.A.Ryan,
and
M.N.James
(2003).
Unbound form of tomato inhibitor-II reveals interdomain flexibility and conformational variability in the reactive site loops.
|
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J Biol Chem,
278,
31391-31400.
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PDB code:
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J.R.Bradford,
and
D.R.Westhead
(2003).
Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem.
|
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Protein Sci,
12,
2099-2103.
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M.Laskowski,
M.A.Qasim,
and
Z.Yi
(2003).
Additivity-based prediction of equilibrium constants for some protein-protein associations.
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| |
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13,
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A.Heifetz,
E.Katchalski-Katzir,
and
M.Eisenstein
(2002).
Electrostatics in protein-protein docking.
|
| |
Protein Sci,
11,
571-587.
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M.K.Udo,
and
B.K.Shoichet
(2002).
Protein-protein docking with multiple residue conformations and residue substitutions.
|
| |
Protein Sci,
11,
1393-1408.
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H.S.Park,
Q.Lin,
and
A.D.Hamilton
(2002).
Modulation of protein-protein interactions by synthetic receptors: design of molecules that disrupt serine protease-proteinaceous inhibitor interaction.
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| |
Proc Natl Acad Sci U S A,
99,
5105-5109.
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K.Anand,
G.J.Palm,
J.R.Mesters,
S.G.Siddell,
J.Ziebuhr,
and
R.Hilgenfeld
(2002).
Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain.
|
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EMBO J,
21,
3213-3224.
|
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PDB code:
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R.E.Georgescu,
E.G.Alexov,
and
M.R.Gunner
(2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
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| |
Biophys J,
83,
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A.Patthy,
L.Gráf,
and
A.Perczel
(2002).
Comparative structure analysis of proteinase inhibitors from the desert locust, Schistocerca gregaria.
|
| |
Eur J Biochem,
269,
527-537.
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PDB codes:
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A.Roussel,
M.Mathieu,
A.Dobbs,
B.Luu,
C.Cambillau,
and
C.Kellenberger
(2001).
Complexation of two proteic insect inhibitors to the active site of chymotrypsin suggests decoupled roles for binding and selectivity.
|
| |
J Biol Chem,
276,
38893-38898.
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PDB codes:
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J.Song,
and
J.L.Markley
(2001).
NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: changes in the (1)H, (13)C and (15)N NMR chemical shifts of turkey ovomucoid third domain upon binding to bovine chymotrypsin A(alpha).
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J Mol Recognit,
14,
166-171.
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K.W.Burdick,
S.Toba,
M.M.Young,
A.G.Skillman,
X.Zou,
J.R.Arnold,
and
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(2001).
Design, docking, and evaluation of multiple libraries against multiple targets.
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Proteins,
42,
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S.M.Lu,
W.Lu,
M.A.Qasim,
S.Anderson,
I.Apostol,
W.Ardelt,
T.Bigler,
Y.W.Chiang,
J.Cook,
M.N.James,
I.Kato,
C.Kelly,
W.Kohr,
T.Komiyama,
T.Y.Lin,
M.Ogawa,
J.Otlewski,
S.J.Park,
S.Qasim,
M.Ranjbar,
M.Tashiro,
N.Warne,
H.Whatley,
A.Wieczorek,
M.Wieczorek,
T.Wilusz,
R.Wynn,
W.Zhang,
and
M.Laskowski
(2001).
Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases.
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Proc Natl Acad Sci U S A,
98,
1410-1415.
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D.W.Ritchie,
and
G.J.Kemp
(2000).
Protein docking using spherical polar Fourier correlations.
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| |
Proteins,
39,
178-194.
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L.I.Krishtalik,
and
V.V.Topolev
(2000).
Effects of medium polarization and pre-existing field on activation energy of enzymatic charge-transfer reactions.
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Biochim Biophys Acta,
1459,
88.
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M.M.Cherney,
N.I.Tarasova,
P.A.Bartlett,
J.E.Hanson,
and
M.N.James
(2000).
Structural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog.
|
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Acta Crystallogr D Biol Crystallogr,
56,
272-279.
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PDB code:
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R.Günther,
S.Thust,
H.J.Hofmann,
and
F.Bordusa
(2000).
Trypsin-specific acyl-4-guanidinophenyl esters for alpha-chymotrypsin-catalysed reactions computational predictions, hydrolyses, and peptide bond formation.
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Eur J Biochem,
267,
3496-3501.
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H.A.Gabb,
and
M.J.Sternberg
(1999).
Use of pair potentials across protein interfaces in screening predicted docked complexes.
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| |
Proteins,
35,
364-373.
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H.Czapinska,
and
J.Otlewski
(1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
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Eur J Biochem,
260,
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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,
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M.A.Qasim,
S.M.Lu,
J.Ding,
K.S.Bateman,
M.N.James,
S.Anderson,
J.Song,
J.L.Markley,
P.J.Ganz,
C.W.Saunders,
and
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(1999).
Thermodynamic criterion for the conformation of P1 residues of substrates and of inhibitors in complexes with serine proteinases.
|
| |
Biochemistry,
38,
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T.Nose,
Y.Yamauchi,
and
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(1999).
Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/pie interaction.
|
| |
Biopolymers,
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H.Rubin,
and
D.W.Christianson
(1998).
Engineering an anion-binding cavity in antichymotrypsin modulates the "spring-loaded" serpin-protease interaction.
|
| |
Biochemistry,
37,
3297-3304.
|
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PDB codes:
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J.Polanowska,
I.Krokoszynska,
H.Czapinska,
W.Watorek,
M.Dadlez,
and
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(1998).
Specificity of human cathepsin G.
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Biochim Biophys Acta,
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C.Qian,
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R.Déziel,
C.Yoakim,
and
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(1998).
Conserved mode of peptidomimetic inhibition and substrate recognition of human cytomegalovirus protease.
|
| |
Nat Struct Biol,
5,
819-826.
|
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PDB code:
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T.Asao,
K.Takahashi,
and
M.Tashiro
(1998).
Interaction of second and third domains of Japanese quail ovomucoid with ten mammalian trypsins.
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| |
Biochim Biophys Acta,
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B.Galunsky,
S.Ignatova,
and
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(1997).
Temperature effects on S1- and S'1-enantioselectivity of alpha-chymotrypsin.
|
| |
Biochim Biophys Acta,
1343,
130-138.
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E.Menegatti,
P.Ascenzi,
and
M.Bolognesi
(1997).
Crystal structure of the bovine alpha-chymotrypsin:Kunitz inhibitor complex. An example of multiple protein:protein recognition sites.
|
| |
J Mol Recognit,
10,
26-35.
|
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PDB code:
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|
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|
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C.S.Cassidy,
J.Lin,
and
P.A.Frey
(1997).
A new concept for the mechanism of action of chymotrypsin: the role of the low-barrier hydrogen bond.
|
| |
Biochemistry,
36,
4576-4584.
|
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|
E.Hohenester,
P.Maurer,
and
R.Timpl
(1997).
Crystal structure of a pair of follistatin-like and EF-hand calcium-binding domains in BM-40.
|
| |
EMBO J,
16,
3778-3786.
|
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PDB code:
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E.M.Bergmann,
S.C.Mosimann,
M.M.Chernaia,
B.A.Malcolm,
and
M.N.James
(1997).
The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition.
|
| |
J Virol,
71,
2436-2448.
|
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PDB codes:
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|
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G.T.DeKoster,
and
A.D.Robertson
(1997).
Thermodynamics of unfolding for Kazal-type serine protease inhibitors: entropic stabilization of ovomucoid first domain by glycosylation.
|
| |
Biochemistry,
36,
2323-2331.
|
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|
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M.A.Qasim,
P.J.Ganz,
C.W.Saunders,
K.S.Bateman,
M.N.James,
and
M.Laskowski
(1997).
Interscaffolding additivity. Association of P1 variants of eglin c and of turkey ovomucoid third domain with serine proteinases.
|
| |
Biochemistry,
36,
1598-1607.
|
|
|
|
|
|
|
M.A.Schumacher,
A.Glasfeld,
H.Zalkin,
and
R.G.Brennan
(1997).
The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity.
|
| |
J Biol Chem,
272,
22648-22653.
|
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PDB code:
|
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|
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|
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T.Kurth,
D.Ullmann,
H.D.Jakubke,
and
L.Hedstrom
(1997).
Converting trypsin to chymotrypsin: structural determinants of S1' specificity.
|
| |
Biochemistry,
36,
10098-10104.
|
|
|
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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shown on the right.
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