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PDBsum entry 1aix
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Blood coagulation/hydrolase inhibitor
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PDB id
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1aix
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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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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Authors
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W.Bode,
D.Turk,
A.Karshikov.
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Ref.
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Protein Sci, 1992,
1,
426-471.
[DOI no: ]
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PubMed id
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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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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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Secondary reference #1
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Title
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Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-Directed inhibitors.
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Authors
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D.W.Banner,
P.Hadváry.
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Ref.
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J Biol Chem, 1991,
266,
20085-20093.
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PubMed id
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