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Contents |
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* Residue conservation analysis
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PDB id:
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Blood coagulation/hydrolase inhibitor
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Title:
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Human alpha-thrombin ternary complex with exosite inhibitor hirugen and active site inhibitor phch2oco-d-dpa-pro-boroval
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Structure:
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Alpha-thrombin (small subunit). Chain: l. Alpha-thrombin (large subunit). Chain: h. Hirugen. Chain: i. Fragment: residues 55 - 64
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Tissue: plasma. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421
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Biol. unit:
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Monomer (from PDB file)
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Resolution:
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2.10Å
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R-factor:
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0.170
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R-free:
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0.230
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Authors:
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E.Skordalakes,G.Dodson,S.Elgendy,C.A.Goodwin,D.Green,R.Tyrrel, M.F.Scully,J.Freyssinet,V.V.Kakkar,J.Deadman
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Key ref:
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W.Bode
et al.
(1992).
The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.
Protein Sci,
1,
426-471.
PubMed id:
DOI:
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Date:
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30-Apr-97
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Release date:
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15-Oct-97
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PROCHECK
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Headers
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References
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Enzyme class:
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Chains L, H:
E.C.3.4.21.5
- thrombin.
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Reaction:
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Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
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DOI no:
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Protein Sci
1:426-471
(1992)
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PubMed id:
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The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.
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W.Bode,
D.Turk,
A.Karshikov.
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ABSTRACT
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Thrombin is a multifunctional serine proteinase that plays a key role in
coagulation while exhibiting several other key cellular bioregulatory functions.
The X-ray crystal structure of human alpha-thrombin was determined in its
complex with the specific thrombin inhibitor D-Phe-Pro-Arg chloromethylketone
(PPACK) using Patterson search methods and a search model derived from
trypsinlike proteinases of known spatial structure (Bode, W., Mayr, I., Baumann,
U., Huber, R., Stone, S.R., & Hofsteenge, J., 1989, EMBO J. 8, 3467-3475).
The crystallographic refinement of the PPACK-thrombin model has now been
completed at an R value of 0.156 (8 to 1.92 A); in particular, the amino- and
the carboxy-termini of the thrombin A-chain are now defined and all side-chain
atoms localized; only proline 37 was found to be in a cis-peptidyl conformation.
The thrombin B-chain exhibits the characteristic polypeptide fold of trypsinlike
serine proteinases; 195 residues occupy topologically equivalent positions with
residues in bovine trypsin and 190 with those in bovine chymotrypsin with a
root-mean-square (r.m.s.) deviation of 0.8 A for their alpha-carbon atoms. Most
of the inserted residues constitute novel surface loops. A chymotrypsinogen
numbering is suggested for thrombin based on the topological equivalences. The
thrombin A-chain is arranged in a boomeranglike shape against the B-chain
globule opposite to the active site; it resembles somewhat the propeptide of
chymotrypsin(ogen) and is similarly not involved in substrate and inhibitor
binding. Thrombin possesses an exceptionally large proportion of charged
residues. The negatively and positively charged residues are not distributed
uniformly over the whole molecule, but are clustered to form a sandwichlike
electrostatic potential; in particular, two extended patches of mainly
positively charged residues occur close to the carboxy-terminal B-chain helix
(forming the presumed heparin-binding site) and on the surface of loop segment
70-80 (the fibrin[ogen] secondary binding exosite), respectively; the negatively
charged residues are more clustered in the ringlike region between both poles,
particularly around the active site. Several of the charged residues are
involved in salt bridges; most are on the surface, but 10 charged protein groups
form completely buried salt bridges and clusters. These electrostatic
interactions play a particularly important role in the intrachain stabilization
of the A-chain, in the coherence between the A- and the B-chain, and in the
surface structure of the fibrin(ogen) secondary binding exosite (loop segment
67-80).(ABSTRACT TRUNCATED AT 400 WORDS)
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Selected figure(s)
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Figure 3.
Fig. 3. Tosyl-m-amidinophenylalanyl-piperidine (thickconnections), NAPAP (mediumconnections),and MQPA (thincon-
nections)boundtotheactivesite of humana-thrombindisplayedtogetherwiththeConnollysurface f thrombin(Turk et al.,
1991). The naphthyl/toluene/chinolyl groups of theinhibitorsinteractwiththearyl-bindingsiteofthrombin;thesidechains
ofthe m- and thep-amidinophenylalanyl residues andofthe arginylresidueenterthespecificitypocketfrom slightly differing
sites; the S2 subsiteofthrombin is occupiedtodifferentextentsbythe(partiallysubstituted)piperidinemoieties.The viewis
similartothestandard view of Figure .
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Figure 30.
Fig. 30. Luzzatiplot f thefinalthrombinmodelafterX-PLOR
refinement.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(1992,
1,
426-471)
copyright 1992.
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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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M.C.Maurer
(2011).
Switching cation-binding loops paves the way for redesigning allosteric activation.
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Proc Natl Acad Sci U S A,
108,
5145-5146.
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A.M.Tanaka-Azevedo,
K.Morais-Zani,
R.J.Torquato,
and
A.S.Tanaka
(2010).
Thrombin inhibitors from different animals.
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J Biomed Biotechnol,
2010,
641025.
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H.L.de Amorim,
P.A.Netz,
and
J.A.Guimarães
(2010).
Thrombin allosteric modulation revisited: a molecular dynamics study.
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J Mol Model,
16,
725-735.
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M.A.Jadhav,
G.Isetti,
T.A.Trumbo,
and
M.C.Maurer
(2010).
Effects of introducing fibrinogen Aalpha character into the factor XIII activation peptide segment.
|
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Biochemistry,
49,
2918-2924.
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|
|
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|
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N.J.Mutch,
T.Myles,
L.L.Leung,
and
J.H.Morrissey
(2010).
Polyphosphate binds with high affinity to exosite II of thrombin.
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J Thromb Haemost,
8,
548-555.
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|
|
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|
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R.De Marco,
M.L.Di Gioia,
A.Leggio,
A.Liguori,
F.Perri,
C.Siciliano,
and
M.C.Viscomi
(2010).
A new non-natural arginine-like amino acid derivative with a sulfamoyl group in the side-chain.
|
| |
Amino Acids,
38,
691-700.
|
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|
|
|
|
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S.Sarilla,
S.Y.Habib,
D.V.Kravtsov,
A.Matafonov,
D.Gailani,
and
I.M.Verhamme
(2010).
Sucrose octasulfate selectively accelerates thrombin inactivation by heparin cofactor II.
|
| |
J Biol Chem,
285,
8278-8289.
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|
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|
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G.Spraggon,
M.Hornsby,
A.Shipway,
D.C.Tully,
B.Bursulaya,
H.Danahay,
J.L.Harris,
and
S.A.Lesley
(2009).
Active site conformational changes of prostasin provide a new mechanism of protease regulation by divalent cations.
|
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Protein Sci,
18,
1081-1094.
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PDB codes:
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I.M.Kovach,
P.Kelley,
C.Eddy,
F.Jordan,
and
A.Baykal
(2009).
Proton bridging in the interactions of thrombin with small inhibitors.
|
| |
Biochemistry,
48,
7296-7304.
|
|
|
|
|
|
|
L.O.Mosnier,
A.Zampolli,
E.J.Kerschen,
R.A.Schuepbach,
Y.Banerjee,
J.A.Fernández,
X.V.Yang,
M.Riewald,
H.Weiler,
Z.M.Ruggeri,
and
J.H.Griffin
(2009).
Hyperantithrombotic, noncytoprotective Glu149Ala-activated protein C mutant.
|
| |
Blood,
113,
5970-5978.
|
|
|
|
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|
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T.M.Sabo,
and
M.C.Maurer
(2009).
Biophysical investigation of GpIbalpha binding to thrombin anion binding exosite II.
|
| |
Biochemistry,
48,
7110-7122.
|
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|
|
|
|
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W.Niu,
Z.Chen,
L.A.Bush-Pelc,
A.Bah,
P.S.Gandhi,
and
E.Di Cera
(2009).
Mutant N143P reveals how Na+ activates thrombin.
|
| |
J Biol Chem,
284,
36175-36185.
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PDB codes:
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A.Poyarkov,
X.Rocabayera,
S.Poyarkova,
and
V.Kukhar
(2008).
Influence of aromatic and aliphatic moieties on thrombin inhibitors potency.
|
| |
Open Biochem J,
2,
143-149.
|
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|
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|
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A.Venceslá,
M.A.Corral-Rodríguez,
M.Baena,
M.Cornet,
M.Domènech,
M.Baiget,
P.Fuentes-Prior,
and
E.F.Tizzano
(2008).
Identification of 31 novel mutations in the F8 gene in Spanish hemophilia A patients: structural analysis of 20 missense mutations suggests new intermolecular binding sites.
|
| |
Blood,
111,
3468-3478.
|
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|
|
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E.Di Cera
(2008).
Thrombin.
|
| |
Mol Aspects Med,
29,
203-254.
|
|
|
|
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|
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F.C.Kurschus,
E.Fellows,
E.Stegmann,
and
D.E.Jenne
(2008).
Granzyme B delivery via perforin is restricted by size, but not by heparan sulfate-dependent endocytosis.
|
| |
Proc Natl Acad Sci U S A,
105,
13799-13804.
|
|
|
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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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|
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M.E.Papaconstantinou,
A.Bah,
and
E.Di Cera
(2008).
Role of the A chain in thrombin function.
|
| |
Cell Mol Life Sci,
65,
1943-1947.
|
|
|
|
|
|
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M.T.Nieman,
F.Burke,
M.Warnock,
Y.Zhou,
J.Sweigart,
A.Chen,
D.Ricketts,
B.R.Lucchesi,
Z.Chen,
E.Di Cera,
J.Hilfinger,
J.S.Kim,
H.I.Mosberg,
and
A.H.Schmaier
(2008).
Thrombostatin FM compounds: direct thrombin inhibitors - mechanism of action in vitro and in vivo.
|
| |
J Thromb Haemost,
6,
837-845.
|
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|
PDB code:
|
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|
|
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|
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N.Singh,
and
J.M.Briggs
(2008).
Molecular dynamics simulations of Factor Xa: insight into conformational transition of its binding subsites.
|
| |
Biopolymers,
89,
1104-1113.
|
|
|
|
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|
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P.S.Gandhi,
Z.Chen,
F.S.Mathews,
and
E.Di Cera
(2008).
Structural identification of the pathway of long-range communication in an allosteric enzyme.
|
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Proc Natl Acad Sci U S A,
105,
1832-1837.
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PDB codes:
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S.B.Long,
M.B.Long,
R.R.White,
and
B.A.Sullenger
(2008).
Crystal structure of an RNA aptamer bound to thrombin.
|
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RNA,
14,
2504-2512.
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PDB code:
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|
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T.Myles,
and
L.L.Leung
(2008).
Thrombin hydrolysis of human osteopontin is dependent on thrombin anion-binding exosites.
|
| |
J Biol Chem,
283,
17789-17796.
|
|
|
|
|
|
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A.Bah,
Z.Chen,
L.A.Bush-Pelc,
F.S.Mathews,
and
E.Di Cera
(2007).
Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.
|
| |
Proc Natl Acad Sci U S A,
104,
11603-11608.
|
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PDB codes:
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D.Blomberg,
T.Fex,
Y.Xue,
K.Brickmann,
and
J.Kihlberg
(2007).
Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold.
|
| |
Org Biomol Chem,
5,
2599-2605.
|
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PDB code:
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E.Di Cera,
M.J.Page,
A.Bah,
L.A.Bush-Pelc,
and
L.C.Garvey
(2007).
Thrombin allostery.
|
| |
Phys Chem Chem Phys,
9,
1291-1306.
|
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E.Rovida,
G.Merati,
P.D'Ursi,
S.Zanardelli,
F.Marino,
G.Fontana,
G.Castaman,
and
E.M.Faioni
(2007).
Identification and computationally-based structural interpretation of naturally occurring variants of human protein C.
|
| |
Hum Mutat,
28,
345-355.
|
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|
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J.T.Crawley,
S.Zanardelli,
C.K.Chion,
and
D.A.Lane
(2007).
The central role of thrombin in hemostasis.
|
| |
J Thromb Haemost,
5,
95.
|
|
|
|
|
|
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M.Debela,
P.Hess,
V.Magdolen,
N.M.Schechter,
T.Steiner,
R.Huber,
W.Bode,
and
P.Goettig
(2007).
Chymotryptic specificity determinants in the 1.0 A structure of the zinc-inhibited human tissue kallikrein 7.
|
| |
Proc Natl Acad Sci U S A,
104,
16086-16091.
|
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PDB codes:
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M.T.Nieman,
and
A.H.Schmaier
(2007).
Interaction of thrombin with PAR1 and PAR4 at the thrombin cleavage site.
|
| |
Biochemistry,
46,
8603-8610.
|
|
|
|
|
|
|
P.E.Bock,
P.Panizzi,
and
I.M.Verhamme
(2007).
Exosites in the substrate specificity of blood coagulation reactions.
|
| |
J Thromb Haemost,
5,
81-94.
|
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|
|
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|
|
S.Charef,
E.Petit,
D.Barritault,
J.Courty,
and
J.P.Caruelle
(2007).
Effects on coagulation of a synthetic heparan mimetic given intraperitoneally or orally.
|
| |
J Biomed Mater Res A,
83,
1024-1031.
|
|
|
|
|
|
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C.Williams
(2006).
Reverse fingerprinting, similarity searching by group fusion and fingerprint bit importance.
|
| |
Mol Divers,
10,
311-332.
|
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|
|
|
|
|
E.Schweizer,
A.Hoffmann-Röder,
J.A.Olsen,
P.Seiler,
U.Obst-Sander,
B.Wagner,
M.Kansy,
D.W.Banner,
and
F.Diederich
(2006).
Multipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors.
|
| |
Org Biomol Chem,
4,
2364-2375.
|
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PDB codes:
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K.M.Bromfield,
N.S.Quinsey,
P.J.Duggan,
and
R.N.Pike
(2006).
Approaches to selective peptidic inhibitors of factor Xa.
|
| |
Chem Biol Drug Des,
68,
11-19.
|
|
|
|
|
|
|
K.Segers,
J.Rosing,
and
G.A.Nicolaes
(2006).
Structural models of the snake venom factor V activators from Daboia russelli and Daboia lebetina.
|
| |
Proteins,
64,
968-984.
|
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PDB codes:
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L.Yang,
C.Manithody,
and
A.R.Rezaie
(2006).
Activation of protein C by the thrombin-thrombomodulin complex: cooperative roles of Arg-35 of thrombin and Arg-67 of protein C.
|
| |
Proc Natl Acad Sci U S A,
103,
879-884.
|
|
|
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N.Díez,
R.Montes,
A.Alonso,
P.Medina,
S.Navarro,
F.España,
and
J.Hermida
(2006).
Association of increased fibrinogen concentration with impaired activation of anticoagulant protein C.
|
| |
J Thromb Haemost,
4,
398-402.
|
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|
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|
|
P.Panizzi,
R.Friedrich,
P.Fuentes-Prior,
H.K.Kroh,
J.Briggs,
G.Tans,
W.Bode,
and
P.E.Bock
(2006).
Novel fluorescent prothrombin analogs as probes of staphylocoagulase-prothrombin interactions.
|
| |
J Biol Chem,
281,
1169-1178.
|
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|
|
R.De Cristofaro,
A.Carotti,
S.Akhavan,
R.Palla,
F.Peyvandi,
C.Altomare,
and
P.M.Mannucci
(2006).
The natural mutation by deletion of Lys9 in the thrombin A-chain affects the pKa value of catalytic residues, the overall enzyme's stability and conformational transitions linked to Na+ binding.
|
| |
FEBS J,
273,
159-169.
|
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|
|
|
|
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R.Friedrich,
P.Panizzi,
S.Kawabata,
W.Bode,
P.E.Bock,
and
P.Fuentes-Prior
(2006).
Structural basis for reduced staphylocoagulase-mediated bovine prothrombin activation.
|
| |
J Biol Chem,
281,
1188-1195.
|
|
|
PDB code:
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|
|
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|
|
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T.T.Baird,
W.D.Wright,
and
C.S.Craik
(2006).
Conversion of trypsin to a functional threonine protease.
|
| |
Protein Sci,
15,
1229-1238.
|
|
|
|
|
|
|
V.De Filippis,
R.Frasson,
and
A.Fontana
(2006).
3-Nitrotyrosine as a spectroscopic probe for investigating protein protein interactions.
|
| |
Protein Sci,
15,
976-986.
|
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|
|
|
|
|
E.Toyota,
H.Sekizaki,
Y.U.Takahashi,
K.Itoh,
and
K.Tanizawa
(2005).
Amidino-containing Schiff base copper(II) and iron(III) chelates as a thrombin inhibitor.
|
| |
Chem Pharm Bull (Tokyo),
53,
22-26.
|
|
|
|
|
|
|
J.A.Huntington
(2005).
Molecular recognition mechanisms of thrombin.
|
| |
J Thromb Haemost,
3,
1861-1872.
|
|
|
|
|
|
|
K.Hosokawa,
T.Ohnishi,
A.Kawakami,
S.Wakabayashi,
and
T.Koide
(2005).
Chemically modified thrombin and anhydrothrombin that differentiate macromolecular substrates of thrombin.
|
| |
J Thromb Haemost,
3,
2703-2711.
|
|
|
|
|
|
|
M.J.Page,
R.T.Macgillivray,
and
E.Di Cera
(2005).
Determinants of specificity in coagulation proteases.
|
| |
J Thromb Haemost,
3,
2401-2408.
|
|
|
|
|
|
|
W.Bode
(2005).
The structure of thrombin, a chameleon-like proteinase.
|
| |
J Thromb Haemost,
3,
2379-2388.
|
|
|
|
|
|
|
A.Dementiev,
M.Petitou,
J.M.Herbert,
and
P.G.Gettins
(2004).
The ternary complex of antithrombin-anhydrothrombin-heparin reveals the basis of inhibitor specificity.
|
| |
Nat Struct Mol Biol,
11,
863-867.
|
|
|
PDB code:
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|
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|
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C.A.Kontogiorgis,
and
D.Hadjipavlou-Litina
(2004).
Current trends in quantitative structure activity relationships on FXa inhibitors: evaluation and comparative analysis.
|
| |
Med Res Rev,
24,
687-747.
|
|
|
|
|
|
|
G.Isetti,
and
M.C.Maurer
(2004).
Probing thrombin's ability to accommodate a V34F substitution within the factor XIII activation peptide segment (28-41).
|
| |
J Pept Res,
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G.Amiconi,
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M.Adler,
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Biochemistry,
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N.Y.Chirgadze,
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R.Krishnan,
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Acta Crystallogr D Biol Crystallogr,
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Acta Crystallogr D Biol Crystallogr,
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A.C.Pike,
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Proc Natl Acad Sci U S A,
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A.Lombardi,
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Protein Sci,
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A.Lombardi,
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Biopolymers,
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Biochemistry,
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I.M.Francischetti,
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Biochemistry,
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Acta Crystallogr D Biol Crystallogr,
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PDB codes:
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M.C.Maurer,
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M.Whitlow,
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Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin.
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Acta Crystallogr D Biol Crystallogr,
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PDB codes:
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R.D.Smith,
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Eur J Biochem,
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Hirunorms are true hirudin mimetics. The crystal structure of human alpha-thrombin-hirunorm V complex.
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PDB code:
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J.Y.Trosset,
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Acta Crystallogr D Biol Crystallogr,
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PDB code:
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K.R.Dharmawardana,
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Biochemistry,
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Novel natural product 5,5-trans-lactone inhibitors of human alpha-thrombin: mechanism of action and structural studies.
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Biochemistry,
37,
6645-6657.
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PDB codes:
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R.Krishnan,
E.Zhang,
K.Hakansson,
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Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.
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Biochemistry,
37,
12094-12103.
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PDB codes:
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S.R.Presnell,
G.S.Patil,
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J.M.Conley,
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C.M.Kam,
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Oxyanion-mediated inhibition of serine proteases.
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Biochemistry,
37,
17068-17081.
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PDB codes:
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V.De Filippis,
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A.Vindigni,
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Synthesis and characterization of more potent analogues of hirudin fragment 1-47 containing non-natural amino acids.
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Biochemistry,
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A.R.Rezaie,
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Biochemistry,
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A.R.Rezaie
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Biochemistry,
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A.Vindigni,
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E.A.Komives,
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Biochemistry,
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A.Vindigni,
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EMBO J,
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PDB code:
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J.J.Slon-Usakiewicz,
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Biochemistry,
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Protein Sci,
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PDB codes:
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M.Renatus,
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Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage.
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Biochemistry,
36,
13483-13493.
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PDB code:
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M.Renatus,
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Lysine 156 promotes the anomalous proenzyme activity of tPA: X-ray crystal structure of single-chain human tPA.
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EMBO J,
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PDB code:
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P.Fuentes-Prior,
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W.D.Schleuning,
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Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug.
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Proc Natl Acad Sci U S A,
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PDB code:
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T.Kurth,
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Biochemistry,
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Biochemistry,
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Eur J Biochem,
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EMBO J,
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PDB code:
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B.F.Le Bonniec,
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Biochemistry,
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Biochemistry,
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15N and 1H NMR spectroscopy of the catalytic histidine in chloromethyl ketone-inhibited complexes of serine proteases.
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Biochemistry,
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Biochemistry,
35,
3147-3155.
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PDB codes:
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|
J.Féthière,
Y.Tsuda,
R.Coulombe,
Y.Konishi,
and
M.Cygler
(1996).
Crystal structure of two new bifunctional nonsubstrate type thrombin inhibitors complexed with human alpha-thrombin.
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Protein Sci,
5,
1174-1183.
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J.H.Matthews,
R.Krishnan,
M.J.Costanzo,
B.E.Maryanoff,
and
A.Tulinsky
(1996).
Crystal structures of thrombin with thiazole-containing inhibitors: probes of the S1' binding site.
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| |
Biophys J,
71,
2830-2839.
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PDB codes:
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|
M.Tsiang,
L.R.Paborsky,
W.X.Li,
A.K.Jain,
C.T.Mao,
K.E.Dunn,
D.W.Lee,
S.Y.Matsumura,
M.D.Matteucci,
S.E.Coutré,
L.L.Leung,
and
C.S.Gibbs
(1996).
Protein engineering thrombin for optimal specificity and potency of anticoagulant activity in vivo.
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| |
Biochemistry,
35,
16449-16457.
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R.Bar-Shavit,
M.Maoz,
Y.Ginzburg,
and
I.Vlodavsky
(1996).
Specific involvement of glypican in thrombin adhesive properties.
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J Cell Biochem,
61,
278-291.
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R.Krishnan,
A.Tulinsky,
G.P.Vlasuk,
D.Pearson,
P.Vallar,
P.Bergum,
T.K.Brunck,
and
W.C.Ripka
(1996).
Synthesis, structure, and structure-activity relationships of divalent thrombin inhibitors containing an alpha-keto-amide transition-state mimetic.
|
| |
Protein Sci,
5,
422-433.
|
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|
PDB code:
|
|
|
|
|
|
|
|
T.Mather,
V.Oganessyan,
P.Hof,
R.Huber,
S.Foundling,
C.Esmon,
and
W.Bode
(1996).
The 2.8 A crystal structure of Gla-domainless activated protein C.
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| |
EMBO J,
15,
6822-6831.
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PDB code:
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|
V.Arocas,
R.B.Zingali,
M.C.Guillin,
C.Bon,
and
M.Jandrot-Perrus
(1996).
Bothrojaracin: a potent two-site-directed thrombin inhibitor.
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| |
Biochemistry,
35,
9083-9089.
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V.Ganesh,
A.Y.Lee,
J.Clardy,
and
A.Tulinsky
(1996).
Comparison of the structures of the cyclotheonamide A complexes of human alpha-thrombin and bovine beta-trypsin.
|
| |
Protein Sci,
5,
825-835.
|
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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.
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| |
Biochemistry,
35,
9690-9699.
|
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A.Bezeaud,
T.Miyata,
D.Helley,
Y.Z.Zeng,
H.Kato,
M.F.Aillaud,
I.Juhan-Vague,
and
M.C.Guillin
(1995).
Functional consequences of the Ser334-->Pro mutation in a human factor X variant (factor XMarseille).
|
| |
Eur J Biochem,
234,
140-147.
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A.van de Locht,
D.Lamba,
M.Bauer,
R.Huber,
T.Friedrich,
B.Kröger,
W.Höffken,
and
W.Bode
(1995).
Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin.
|
| |
EMBO J,
14,
5149-5157.
|
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PDB codes:
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|
|
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|
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|
|
E.R.Guinto,
A.Vindigni,
Y.M.Ayala,
Q.D.Dang,
and
E.Di Cera
(1995).
Identification of residues linked to the slow-->fast transition of thrombin.
|
| |
Proc Natl Acad Sci U S A,
92,
11185-11189.
|
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H.Brandstetter,
M.Bauer,
R.Huber,
P.Lollar,
and
W.Bode
(1995).
X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.
|
| |
Proc Natl Acad Sci U S A,
92,
9796-9800.
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|
PDB code:
|
|
|
|
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|
|
|
C.L.Fisher,
J.S.Greengard,
and
J.H.Griffin
(1994).
Models of the serine protease domain of the human antithrombotic plasma factor activated protein C and its zymogen.
|
| |
Protein Sci,
3,
588-599.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.P.Sheehan,
and
J.E.Sadler
(1994).
Molecular mapping of the heparin-binding exosite of thrombin.
|
| |
Proc Natl Acad Sci U S A,
91,
5518-5522.
|
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J.Vijayalakshmi,
K.P.Padmanabhan,
K.G.Mann,
and
A.Tulinsky
(1994).
The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin.
|
| |
Protein Sci,
3,
2254-2271.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.E.Donate,
E.Gherardi,
N.Srinivasan,
R.Sowdhamini,
S.Aparicio,
and
T.L.Blundell
(1994).
Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP).
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| |
Protein Sci,
3,
2378-2394.
|
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M.F.Kubik,
A.W.Stephens,
D.Schneider,
R.A.Marlar,
and
D.Tasset
(1994).
High-affinity RNA ligands to human alpha-thrombin.
|
| |
Nucleic Acids Res,
22,
2619-2626.
|
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M.Picozzi,
R.Landolfi,
and
R.De Cristofaro
(1994).
Effects of protons on the thrombin-fibrinogen interaction.
|
| |
Eur J Biochem,
219,
1013-1021.
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U.Egner,
G.A.Hoyer,
and
W.D.Schleuning
(1994).
Rational design of hirulog-type inhibitors of thrombin.
|
| |
J Comput Aided Mol Des,
8,
479-490.
|
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V.Z.Spassov,
A.D.Karshikoff,
and
R.Ladenstein
(1994).
Optimization of the electrostatic interactions in proteins of different functional and folding type.
|
| |
Protein Sci,
3,
1556-1569.
|
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|
|
A.I.Wacey,
S.Pemberton,
D.N.Cooper,
V.V.Kakkar,
and
E.G.Tuddenham
(1993).
A molecular model of the serine protease domain of activated protein C: application to the study of missense mutations causing protein C deficiency.
|
| |
Br J Haematol,
84,
290-300.
|
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|
|
|
|
|
B.E.Maryanoff,
X.Qiu,
K.P.Padmanabhan,
A.Tulinsky,
H.R.Almond,
P.Andrade-Gordon,
M.N.Greco,
J.A.Kauffman,
K.C.Nicolaou,
and
A.Liu
(1993).
Molecular basis for the inhibition of human alpha-thrombin by the macrocyclic peptide cyclotheonamide A.
|
| |
Proc Natl Acad Sci U S A,
90,
8048-8052.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.C.Whinna,
and
F.C.Church
(1993).
Interaction of thrombin with antithrombin, heparin cofactor II, and protein C inhibitor.
|
| |
J Protein Chem,
12,
677-688.
|
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|
|
J.P.Priestle,
J.Rahuel,
H.Rink,
M.Tones,
and
M.G.Grütter
(1993).
Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms.
|
| |
Protein Sci,
2,
1630-1642.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Bar-Shavit,
Y.Eskohjido,
J.W.Fenton,
J.D.Esko,
and
I.Vlodavsky
(1993).
Thrombin adhesive properties: induction by plasmin and heparan sulfate.
|
| |
J Cell Biol,
123,
1279-1287.
|
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|
|
A.Karshikov,
W.Bode,
A.Tulinsky,
and
S.R.Stone
(1992).
Electrostatic interactions in the association of proteins: an analysis of the thrombin-hirudin complex.
|
| |
Protein Sci,
1,
727-735.
|
|
|
|
|
|
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
codes are
shown on the right.
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