1pdc

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(New page: 200px<br /><applet load="1pdc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pdc" /> '''REFINED SOLUTION STRUCTURE AND LIGAND-BINDIN...)
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[[Image:1pdc.gif|left|200px]]<br /><applet load="1pdc" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pdc" />
 
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'''REFINED SOLUTION STRUCTURE AND LIGAND-BINDING PROPERTIES OF PDC-109 DOMAIN B. A COLLAGEN-BINDING TYPE II DOMAIN'''<br />
 
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==Overview==
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==REFINED SOLUTION STRUCTURE AND LIGAND-BINDING PROPERTIES OF PDC-109 DOMAIN B. A COLLAGEN-BINDING TYPE II DOMAIN==
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We have determined, via 1H-n.m.r., the solution conformation of the, collagen-binding b-domain of the bovine seminal fluid protein PDC-109, (PDC-109/b). The structure determination is based on 341 interproton, distance estimates and 42 dihedral angle estimates: a set of 24 initial, structures were computed; 12 using the variable target function program, DIANA, and 12 using the metric matrix program DISGEO. These structures, were optimized by restrained energy minimization and dynamic simulated, annealing using the CHARMM and X-PLOR programs. The average pairwise, root-mean-square difference (r.m.s.d) between the optimized DIANA (DISGEO), structures is 0.71 A (0.82 A) for the backbone atoms, and 1.73 A (2.03 A), for all atoms. Both sets of structures exhibit the same global fold, secondary structure and placement of most non-polar side-chains. Two, central antiparallel beta-sheets, which lie roughly perpendicular to each, other, and two irregular loops support a large, partially exposed, hydrophobic surface that defines a putative binding site. A test of a, hybrid relaxation matrix-based distance refinement protocol (MIDGE, program) was performed using a normalized 250 millisecond NOESY spectrum., The resulting distances were input to the molecular mechanics/dynamics, procedures mentioned above in order to optimize the DIANA structures. Our, results indicate that relaxation matrix refinement of distances is most, useful when used conservatively for identifying underestimated distance, constraints. 1H-n.m.r. monitored ligand titration experiments revealed, definite, albeit weak, binding interactions for phenethylamine and leucine, analogs (Ka less than or equal to 25 M-1). Residues perturbed by ligand, binding include Tyr7, Trp26, Tyr33, Asp34 and Trp39. These results suggest, that PDC-109/b may recognize specific leucine and/or isoleucine-containing, sequences within collagen.
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<StructureSection load='1pdc' size='340' side='right'caption='[[1pdc]]' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1pdc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PDC FirstGlance]. <br>
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1PDC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PDC OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pdc OCA], [https://pdbe.org/1pdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pdc RCSB], [https://www.ebi.ac.uk/pdbsum/1pdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pdc ProSAT]</span></td></tr>
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==Reference==
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</table>
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Refined solution structure and ligand-binding properties of PDC-109 domain b. A collagen-binding type II domain., Constantine KL, Madrid M, Banyai L, Trexler M, Patthy L, Llinas M, J Mol Biol. 1992 Jan 5;223(1):281-98. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1731074 1731074]
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== Function ==
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[https://www.uniprot.org/uniprot/SFP1_BOVIN SFP1_BOVIN] Could enhance the fertilizing capacity of bull spermatozoa upon interaction with heparin-like glycosaminoglycans present in the female genital tract. Exhibits both simulatory and inhibitory actions on the release of pituitary gonadotropins.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pd/1pdc_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pdc ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Constantine, K.L.]]
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[[Category: Constantine KL]]
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[[Category: Llinas, M.]]
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[[Category: Llinas M]]
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[[Category: Patthy, L.]]
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[[Category: Patthy L]]
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[[Category: collagen-binding type ii domain]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:42:29 2007''
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Current revision

REFINED SOLUTION STRUCTURE AND LIGAND-BINDING PROPERTIES OF PDC-109 DOMAIN B. A COLLAGEN-BINDING TYPE II DOMAIN

PDB ID 1pdc

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