1m1j
From Proteopedia
(Difference between revisions)
| Line 4: | Line 4: | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1m1j]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jfe 1jfe]. The November 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Fibrin'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_11 10.2210/rcsb_pdb/mom_2006_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M1J FirstGlance]. <br> | <table><tr><td colspan='2'>[[1m1j]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jfe 1jfe]. The November 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Fibrin'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_11 10.2210/rcsb_pdb/mom_2006_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M1J FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr> | |
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1j OCA], [https://pdbe.org/1m1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m1j RCSB], [https://www.ebi.ac.uk/pdbsum/1m1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m1j ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1j OCA], [https://pdbe.org/1m1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m1j RCSB], [https://www.ebi.ac.uk/pdbsum/1m1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m1j ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/FIBA_CHICK FIBA_CHICK] Fibrinogen has a double function: yielding monomers that polymerize into fibrin and acting as a cofactor in platelet aggregation. | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 20: | Line 20: | ||
</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=1m1j ConSurf]. | </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=1m1j ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The crystal structure of native chicken fibrinogen (320 kDa) complexed with two synthetic peptides has been determined at a resolution of 2.7 A. The structure provides the first atomic-resolution view of the polypeptide chain arrangement in the central domain where the two halves of the molecule are joined, as well as of a putative thrombin-binding site. The amino-terminal segments of the alpha and beta chains, including fibrinopeptides A and B, are not visible in electron density maps, however, and must be highly disordered. The alphaC domain is also very disordered. A residue by residue analysis of the coiled coils with regard to temperature factor shows a strong correlation between mobility and plasmin attack sites. It is concluded that structural flexibility is an inherent feature of fibrinogen that plays a key role in both its conversion to fibrin and its subsequent destruction by plasmin. | ||
| - | |||
| - | Crystal structure of native chicken fibrinogen at 2.7 A resolution.,Yang Z, Kollman JM, Pandi L, Doolittle RF Biochemistry. 2001 Oct 23;40(42):12515-23. PMID:11601975<ref>PMID:11601975</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1m1j" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Fibrinogen|Fibrinogen]] | *[[Fibrinogen|Fibrinogen]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| Line 40: | Line 29: | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: RCSB PDB Molecule of the Month]] | [[Category: RCSB PDB Molecule of the Month]] | ||
| - | [[Category: Doolittle | + | [[Category: Doolittle RF]] |
| - | [[Category: Kollman | + | [[Category: Kollman JM]] |
| - | [[Category: Pandi | + | [[Category: Pandi L]] |
| - | [[Category: Yang | + | [[Category: Yang Z]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Crystal structure of native chicken fibrinogen with two different bound ligands
| |||||||||||
