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1lwu

From Proteopedia

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[[Image:1lwu.gif|left|200px]]<br /><applet load="1lwu" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1lwu, resolution 2.80&Aring;" />
 
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'''Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide'''<br />
 
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==Overview==
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==Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide==
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The crystal structure of fragment D from lamprey fibrinogen has been determined at 2.8 A resolution. The 89 kDa protein was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens-but not lamprey-corresponds to the B knob exposed by thrombin. Because lamprey fragment D is more than 50% identical in sequence with human fragment D, the structure of which has been reported previously, it was possible to use the method of molecular replacement. The space group of the lamprey crystals is P1; there are four molecules in the unit cell. Although the fragments are packed head to head by the same D:D interface as is observed in other related preparations containing fragments D, the tails are uniquely joined by an unnatural association of the terminal sections of the residual coiled coils from adjacent molecules. Some features of the lamprey structure are clearer than have been observed in previous fragment D structures, including the beta-chain carbohydrate cluster, for one, and the important gamma-chain carboxyl-terminal segment, for another. The most significant differences between the lamprey and human structures occur in connecting loops at the entryways to the beta-chain and gamma-chain binding pockets.
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<StructureSection load='1lwu' size='340' side='right'caption='[[1lwu]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1lwu]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LWU FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></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=1lwu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwu OCA], [https://pdbe.org/1lwu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lwu RCSB], [https://www.ebi.ac.uk/pdbsum/1lwu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwu ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/FIBA1_PETMA FIBA1_PETMA] Fibrinogen has a double function: yielding monomers that polymerize into fibrin and acting as a cofactor in platelet aggregation.
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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/lw/1lwu_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=1lwu ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1LWU is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus] with <scene name='pdbligand=NDG:'>NDG</scene>, <scene name='pdbligand=MAN:'>MAN</scene>, <scene name='pdbligand=NAG:'>NAG</scene>, <scene name='pdbligand=GAL:'>GAL</scene>, <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=NH2:'>NH2</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWU OCA].
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*[[Fibrinogen|Fibrinogen]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide., Yang Z, Spraggon G, Pandi L, Everse SJ, Riley M, Doolittle RF, Biochemistry. 2002 Aug 13;41(32):10218-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12162736 12162736]
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[[Category: Large Structures]]
[[Category: Petromyzon marinus]]
[[Category: Petromyzon marinus]]
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[[Category: Protein complex]]
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[[Category: Doolittle RF]]
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[[Category: Doolittle, R F.]]
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[[Category: Everse SJ]]
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[[Category: Everse, S J.]]
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[[Category: Pandi L]]
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[[Category: Pandi, L.]]
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[[Category: Riley M]]
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[[Category: Riley, M.]]
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[[Category: Spraggon G]]
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[[Category: Spraggon, G.]]
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[[Category: Yang Z]]
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[[Category: Yang, Z.]]
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[[Category: CA]]
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[[Category: GAL]]
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[[Category: MAN]]
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[[Category: NAG]]
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[[Category: NDG]]
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[[Category: NH2]]
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[[Category: coiled coil]]
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[[Category: heterotrimer]]
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[[Category: protein-peptide complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:49:13 2008''
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Current revision

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide

PDB ID 1lwu

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