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PDBsum entry 4sga
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Hydrolase/hydrolase inhibitor
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PDB id
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4sga
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* Residue conservation analysis
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Enzyme class:
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E.C.3.4.21.80
- streptogrisin A.
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Reaction:
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Hydrolysis of proteins with specificity similar to chymotrypsin.
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DOI no:
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J Mol Biol
144:43-88
(1980)
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PubMed id:
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Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 A resolution. A model for serine protease catalysis.
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M.N.James,
A.R.Sielecki,
G.D.Brayer,
L.T.Delbaere,
C.A.Bauer.
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ABSTRACT
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Selected figure(s)
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Figure 3.
FIG:. 3. Difference electron density maps computed with coefficients IE',\ - IP,I. phases hC in the region
ofthe active ite of SGPA. These are fragment maps in which a portin of the molecule was not included in.~
the structure factor calculation.
(a) AcPro-Ala-Pro-Phe-OH, peptide 1, the atoms excluded from the phase calculation were 0' of
Ser195 and th terminal carboxyl oxygen atom of the tetrapeptide product which binds in the oxyanion
bindin site. The 2 largest positive peaks correspond to these expected atomic position. The 3rd peak
just below that for OY of Ser195 corresponds to a water molecule not included in the phasng.
(b) The corresponding atomic model ofthe tetrapeptide aldehyde (onl P, Pro and P, Phe shown) with
the electron ensity for Oy Her195 and the two water moleules 0366 and 0361 which were not mcluded in
the calculation.
In both (a) and (b) the electron density cotour surfaces are kO.23 eA3 and the negative density is
represented by broken lines. This and subsequent Figures have been made with the aid of the MMS-X
interactive graphics (Barry et al., 1976).
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Figure 9.
FIG. 9. Comparison ofthe binding modes ofthe Ac-Pro-Ala-Pro-Phe-OH product (solid, thin lines) and
the aldehyde inhibitor (broken lines). The enzyme conformation is that obseved in complex I. The P, Pro
ring hs a changed coformation in the aldehyde. The carbonyl carbon atom of the aldehyde is I.73 A
distant from Oy of Ser195.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1980,
144,
43-88)
copyright 1980.
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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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G.Gupta,
A.S.Bhaskar,
B.K.Tripathi,
P.Pandey,
M.Boopathi,
P.V.Rao,
B.Singh,
and
R.Vijayaraghavan
(2011).
Supersensitive detection of T-2 toxin by the in situ synthesized π-conjugated molecularly imprinted nanopatterns. An in situ investigation by surface plasmon resonance combined with electrochemistry.
|
| |
Biosens Bioelectron,
26,
2534-2540.
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S.Cui,
J.Wang,
T.Fan,
B.Qin,
L.Guo,
X.Lei,
J.Wang,
M.Wang,
and
Q.Jin
(2011).
Crystal structure of human enterovirus 71 3C protease.
|
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J Mol Biol,
408,
449-461.
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PDB code:
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E.Zakharova,
M.P.Horvath,
and
D.P.Goldenberg
(2009).
Structure of a serine protease poised to resynthesize a peptide bond.
|
| |
Proc Natl Acad Sci U S A,
106,
11034-11039.
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PDB codes:
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K.S.Keating,
S.C.Flores,
M.B.Gerstein,
and
L.A.Kuhn
(2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
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| |
Protein Sci,
18,
359-371.
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|
|
T.C.Terwilliger,
R.W.Grosse-Kunstleve,
P.V.Afonine,
N.W.Moriarty,
P.D.Adams,
R.J.Read,
P.H.Zwart,
and
L.W.Hung
(2008).
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias.
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| |
Acta Crystallogr D Biol Crystallogr,
64,
515-524.
|
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|
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T.R.Sweeney,
N.Roqué-Rosell,
J.R.Birtley,
R.J.Leatherbarrow,
and
S.Curry
(2007).
Structural and mutagenic analysis of foot-and-mouth disease virus 3C protease reveals the role of the beta-ribbon in proteolysis.
|
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J Virol,
81,
115-124.
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PDB code:
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S.Geremia,
M.Campagnolo,
N.Demitri,
and
L.N.Johnson
(2006).
Simulation of diffusion time of small molecules in protein crystals.
|
| |
Structure,
14,
393-400.
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F.Gabel,
M.Weik,
P.Masson,
F.Renault,
D.Fournier,
L.Brochier,
B.P.Doctor,
A.Saxena,
I.Silman,
and
G.Zaccai
(2005).
Effects of soman inhibition and of structural differences on cholinesterase molecular dynamics: a neutron scattering study.
|
| |
Biophys J,
89,
3303-3311.
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K.E.McAuley,
A.Svendsen,
S.A.Patkar,
and
K.S.Wilson
(2004).
Structure of a feruloyl esterase from Aspergillus niger.
|
| |
Acta Crystallogr D Biol Crystallogr,
60,
878-887.
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PDB codes:
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K.Karbstein,
and
D.Herschlag
(2003).
Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function.
|
| |
Proc Natl Acad Sci U S A,
100,
2300-2305.
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P.Masson,
F.Nachon,
C.F.Bartels,
M.T.Froment,
F.Ribes,
C.Matthews,
and
O.Lockridge
(2003).
High activity of human butyrylcholinesterase at low pH in the presence of excess butyrylthiocholine.
|
| |
Eur J Biochem,
270,
315-324.
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C.Hetényi,
and
D.van der Spoel
(2002).
Efficient docking of peptides to proteins without prior knowledge of the binding site.
|
| |
Protein Sci,
11,
1729-1737.
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E.Bianchi,
and
A.Pessi
(2002).
Inhibiting viral proteases: challenges and opportunities.
|
| |
Biopolymers,
66,
101-114.
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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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M.Boncheva,
D.H.Gracias,
H.O.Jacobs,
and
G.M.Whitesides
(2002).
Biomimetic self-assembly of a functional asymmetrical electronic device.
|
| |
Proc Natl Acad Sci U S A,
99,
4937-4940.
|
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P.Ingallinella,
D.Fattori,
S.Altamura,
C.Steinkühler,
U.Koch,
D.Cicero,
R.Bazzo,
R.Cortese,
E.Bianchi,
and
A.Pessi
(2002).
Prime site binding inhibitors of a serine protease: NS3/4A of hepatitis C virus.
|
| |
Biochemistry,
41,
5483-5492.
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W.B.Alkema,
A.J.Dijkhuis,
E.De Vries,
and
D.B.Janssen
(2002).
The role of hydrophobic active-site residues in substrate specificity and acyl transfer activity of penicillin acylase.
|
| |
Eur J Biochem,
269,
2093-2100.
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A.Pessi
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A personal account of the role of peptide research in drug discovery: the case of hepatitis C.
|
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J Pept Sci,
7,
2.
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D.Neidhart,
Y.Wei,
C.Cassidy,
J.Lin,
W.W.Cleland,
and
P.A.Frey
(2001).
Correlation of low-barrier hydrogen bonding and oxyanion binding in transition state analogue complexes of chymotrypsin.
|
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Biochemistry,
40,
2439-2447.
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PDB codes:
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I.Nakanishi,
T.Kinoshita,
A.Sato,
and
T.Tada
(2000).
Structure of porcine pancreatic elastase complexed with FR901277, a novel macrocyclic inhibitor of elastases, at 1.6 A resolution.
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Biopolymers,
53,
434-445.
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PDB code:
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M.R.Gunner,
M.A.Saleh,
E.Cross,
A.ud-Doula,
and
M.Wise
(2000).
Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect.
|
| |
Biophys J,
78,
1126-1144.
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T.Steinmetzer,
M.Batdordshjin,
F.Pineda,
L.Seyfarth,
A.Vogel,
S.Reissmann,
J.Hauptmann,
and
J.Stürzebecher
(2000).
New bivalent thrombin inhibitors with N(alpha)(methyl)arginine at the P1-position.
|
| |
Biol Chem,
381,
603-610.
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H.Czapinska,
and
J.Otlewski
(1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
|
| |
Eur J Biochem,
260,
571-595.
|
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H.M.Murthy,
S.Clum,
and
R.Padmanabhan
(1999).
Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects.
|
| |
J Biol Chem,
274,
5573-5580.
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PDB code:
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C.Steinkühler,
G.Biasiol,
M.Brunetti,
A.Urbani,
U.Koch,
R.Cortese,
A.Pessi,
and
R.De Francesco
(1998).
Product inhibition of the hepatitis C virus NS3 protease.
|
| |
Biochemistry,
37,
8899-8905.
|
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|
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M.Llinàs-Brunet,
M.Bailey,
R.Déziel,
G.Fazal,
V.Gorys,
S.Goulet,
T.Halmos,
R.Maurice,
M.Poirier,
M.A.Poupart,
J.Rancourt,
D.Thibeault,
D.Wernic,
and
D.Lamarre
(1998).
Studies on the C-terminal of hexapeptide inhibitors of the hepatitis C virus serine protease.
|
| |
Bioorg Med Chem Lett,
8,
2719-2724.
|
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|
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P.Ingallinella,
S.Altamura,
E.Bianchi,
M.Taliani,
R.Ingenito,
R.Cortese,
R.De Francesco,
C.Steinkühler,
and
A.Pessi
(1998).
Potent peptide inhibitors of human hepatitis C virus NS3 protease are obtained by optimizing the cleavage products.
|
| |
Biochemistry,
37,
8906-8914.
|
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|
|
B.Bax,
T.L.Blundell,
J.Murray-Rust,
and
N.Q.McDonald
(1997).
Structure of mouse 7S NGF: a complex of nerve growth factor with four binding proteins.
|
| |
Structure,
5,
1275-1285.
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PDB code:
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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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|
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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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J.Xu,
E.Mendez,
P.R.Caron,
C.Lin,
M.A.Murcko,
M.S.Collett,
and
C.M.Rice
(1997).
Bovine viral diarrhea virus NS3 serine proteinase: polyprotein cleavage sites, cofactor requirements, and molecular model of an enzyme essential for pestivirus replication.
|
| |
J Virol,
71,
5312-5322.
|
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|
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P.R.Mittl,
S.Di Marco,
J.F.Krebs,
X.Bai,
D.S.Karanewsky,
J.P.Priestle,
K.J.Tomaselli,
and
M.G.Grütter
(1997).
Structure of recombinant human CPP32 in complex with the tetrapeptide acetyl-Asp-Val-Ala-Asp fluoromethyl ketone.
|
| |
J Biol Chem,
272,
6539-6547.
|
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PDB code:
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R.C.Wilmouth,
I.J.Clifton,
C.V.Robinson,
P.L.Roach,
R.T.Aplin,
N.J.Westwood,
J.Hajdu,
and
C.J.Schofield
(1997).
Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase.
|
| |
Nat Struct Biol,
4,
456-462.
|
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PDB code:
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I.V.Kurinov,
and
R.W.Harrison
(1996).
Two crystal structures of the leupeptin-trypsin complex.
|
| |
Protein Sci,
5,
752-758.
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PDB codes:
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N.C.Singha,
N.Surolia,
and
A.Surolia
(1996).
On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation.
|
| |
Biosci Rep,
16,
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V.L.Nienaber,
L.J.Mersinger,
and
C.A.Kettner
(1996).
Structure-based understanding of ligand affinity using human thrombin as a model system.
|
| |
Biochemistry,
35,
9690-9699.
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C.S.Poornima,
and
P.M.Dean
(1995).
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions.
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J Comput Aided Mol Des,
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C.S.Poornima,
and
P.M.Dean
(1995).
Hydration in drug design. 2. Influence of local site surface shape on water binding.
|
| |
J Comput Aided Mol Des,
9,
513-520.
|
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S.S.Sidhu,
G.B.Kalmar,
L.G.Willis,
and
T.J.Borgford
(1995).
Protease evolution in Streptomyces griseus. Discovery of a novel dimeric enzymes.
|
| |
J Biol Chem,
270,
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|
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B.W.Matthews,
C.S.Craik,
and
H.Neurath
(1994).
Can small cyclic peptides have the activity and specificity of proteolytic enzymes?
|
| |
Proc Natl Acad Sci U S A,
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|
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P.D.Edwards,
and
P.R.Bernstein
(1994).
Synthetic inhibitors of elastase.
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| |
Med Res Rev,
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|
|
P.L.Chau,
and
P.M.Dean
(1994).
Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects.
|
| |
J Comput Aided Mol Des,
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|
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|
|
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|
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P.L.Chau,
and
P.M.Dean
(1994).
Electrostatic complementarity between proteins and ligands. 2. Ligand moieties.
|
| |
J Comput Aided Mol Des,
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|
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|
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|
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P.L.Chau,
and
P.M.Dean
(1994).
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|
| |
J Comput Aided Mol Des,
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|
|
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|
|
S.J.Hubbard,
F.Eisenmenger,
and
J.M.Thornton
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Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
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| |
Protein Sci,
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|
|
|
|
|
|
|
T.N.Bhat,
G.A.Bentley,
G.Boulot,
M.I.Greene,
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F.P.Schwarz,
R.A.Mariuzza,
and
R.J.Poljak
(1994).
Bound water molecules and conformational stabilization help mediate an antigen-antibody association.
|
| |
Proc Natl Acad Sci U S A,
91,
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|
|
|
PDB codes:
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|
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E.Cheah,
G.W.Ashley,
J.Gary,
and
D.Ollis
(1993).
Catalysis by dienelactone hydrolase: a variation on the protease mechanism.
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| |
Proteins,
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|
|
|
|
|
|
|
G.Müller,
M.Gurrath,
M.Kurz,
and
H.Kessler
(1993).
Beta VI turns in peptides and proteins: a model peptide mimicry.
|
| |
Proteins,
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|
|
|
|
|
|
M.Lindahl,
L.A.Svensson,
and
A.Liljas
(1993).
Metal poison inhibition of carbonic anhydrase.
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| |
Proteins,
15,
177-182.
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|
|
|
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|
|
S.Nakagawa,
H.A.Yu,
M.Karplus,
and
H.Umeyama
(1993).
Active site dynamics of acyl-chymotrypsin.
|
| |
Proteins,
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172-194.
|
|
|
|
|
|
|
E.Meyer
(1992).
Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications.
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| |
Protein Sci,
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|
|
|
|
|
|
|
J.S.Richardson,
D.C.Richardson,
N.B.Tweedy,
K.M.Gernert,
T.P.Quinn,
M.H.Hecht,
B.W.Erickson,
Y.Yan,
R.D.McClain,
and
M.E.Donlan
(1992).
Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992.
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| |
Biophys J,
63,
1185-1209.
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|
W.Bode,
and
R.Huber
(1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
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| |
Eur J Biochem,
204,
433-451.
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|
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|
|
J.Rose,
and
F.Eisenmenger
(1991).
A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm.
|
| |
J Mol Evol,
32,
340-354.
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|
|
M.Nilges,
G.M.Clore,
and
A.M.Gronenborn
(1990).
1H-NMR stereospecific assignments by conformational data-base searches.
|
| |
Biopolymers,
29,
813-822.
|
|
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|
|
|
|
M.S.Johnson,
M.J.Sutcliffe,
and
T.L.Blundell
(1990).
Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins.
|
| |
J Mol Evol,
30,
43-59.
|
|
|
|
|
|
|
P.C.Chang,
T.C.Kuo,
A.Tsugita,
and
Y.H.Lee
(1990).
Extracellular metalloprotease gene of Streptomyces cacaoi: structure, nucleotide sequence and characterization of the cloned gene product.
|
| |
Gene,
88,
87-95.
|
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|
|
M.A.Navia,
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J.P.Springer,
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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
