This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1n73

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1n73" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n73, resolution 2.90&Aring;" /> '''Fibrin D-Dimer, Lamp...)
Current revision (08:46, 10 April 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1n73.gif|left|200px]]<br /><applet load="1n73" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1n73, resolution 2.90&Aring;" />
 
-
'''Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE'''<br />
 
-
==Overview==
+
==Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE==
-
The crystal structure of fragment double-D from factor XIII-cross-linked, lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa, covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that of lamprey, corresponds to the, B-knob exposed by thrombin. The structure was determined by molecular, replacement, a recently determined structure of lamprey fragment D being, used as a search model. GHRPam was found in both the gamma- and beta-chain, holes. Unlike the situation with fragment D, the crystal packing of the, cross-linked double-D structure exhibits two different D-D interfaces, each gamma-chain facing gamma-chains on two other molecules. One of these, (interface I) involves the asymmetric interface observed in all other D, fragments and related structures. The other (interface II) encompasses a, completely different set of residues. The two abutments differ in that, interface I results in an "in line" arrangement of abutting molecules and, the interface II in a "zigzag" arrangement. So far as can be determined, (the electron density could only be traced on one side of the, cross-links), it is the gamma-chains of the newly observed zigzag units, (interface II) that are joined by the reciprocal, epsilon-amino-gamma-glutamyl cross-links. Auspiciously, the same novel D-D, interface was observed in two lower-resolution crystal structures of human, double-D preparations that had been crystallized under unusual, circumstances. These observations show that double-D structures are linked, in a way that is sufficiently flexible to accommodate different D-D, interfaces under different circumstances.
+
<StructureSection load='1n73' size='340' side='right'caption='[[1n73]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1n73]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N73 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N73 FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</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></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=1n73 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n73 OCA], [https://pdbe.org/1n73 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n73 RCSB], [https://www.ebi.ac.uk/pdbsum/1n73 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n73 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[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.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n73_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1n73 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1N73 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 NAG and CA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N73 OCA].
+
*[[Fibrin|Fibrin]]
-
 
+
*[[Fibrinogen|Fibrinogen]]
-
==Reference==
+
__TOC__
-
The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface., Yang Z, Pandi L, Doolittle RF, Biochemistry. 2002 Dec 31;41(52):15610-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12501189 12501189]
+
</StructureSection>
 +
[[Category: Homo sapiens]]
 +
[[Category: Large Structures]]
[[Category: Petromyzon marinus]]
[[Category: Petromyzon marinus]]
-
[[Category: Protein complex]]
+
[[Category: Doolittle RF]]
-
[[Category: Doolittle, R.F.]]
+
[[Category: Pandi L]]
-
[[Category: Pandi, L.]]
+
[[Category: Yang Z]]
-
[[Category: Yang, Z.]]
+
-
[[Category: CA]]
+
-
[[Category: NAG]]
+
-
[[Category: isopeptide cross-linked chains; protein-peptide complex]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:00:49 2007''
+

Current revision

Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE

PDB ID 1n73

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1n73"
Personal tools