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1pdc

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[[Image:1pdc.gif|left|200px]]
 
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{{Structure
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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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|PDB= 1pdc |SIZE=350|CAPTION= <scene name='initialview01'>1pdc</scene>
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<StructureSection load='1pdc' size='340' side='right'caption='[[1pdc]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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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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|ACTIVITY=
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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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|GENE=
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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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|DOMAIN=
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</table>
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|RELATEDENTRY=
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pdc OCA], [http://www.ebi.ac.uk/pdbsum/1pdc PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pdc RCSB]</span>
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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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}}
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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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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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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==Overview==
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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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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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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==About this Structure==
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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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1PDC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PDC OCA].
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<div style="clear:both"></div>
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__TOC__
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==Reference==
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</StructureSection>
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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://www.ncbi.nlm.nih.gov/pubmed/1731074 1731074]
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[[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://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:58:09 2008''
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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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