1jan: Difference between revisions

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<StructureSection load='1jan' size='340' side='right'caption='[[1jan]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='1jan' size='340' side='right'caption='[[1jan]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1jan]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JAN FirstGlance]. <br>
<table><tr><td colspan='2'>[[1jan]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JAN 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=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HOA:HYDROXYAMINE'>HOA</scene></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=HOA:HYDROXYAMINE'>HOA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Neutrophil_collagenase Neutrophil collagenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.34 3.4.24.34] </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=1jan FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jan OCA], [https://pdbe.org/1jan PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jan RCSB], [https://www.ebi.ac.uk/pdbsum/1jan PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jan 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=1jan FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jan OCA], [https://pdbe.org/1jan PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jan RCSB], [https://www.ebi.ac.uk/pdbsum/1jan PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jan ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/MMP8_HUMAN MMP8_HUMAN]] Can degrade fibrillar type I, II, and III collagens.  
[https://www.uniprot.org/uniprot/MMP8_HUMAN MMP8_HUMAN] Can degrade fibrillar type I, II, and III collagens.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1jan 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=1jan ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
For the collagenases PMNL-CL and FIB-CL, the presence of the N-terminal Phe79 correlates with an increase in proteolytic activity. We have determined the X-ray crystal structure of the recombinant Phe79-Gly242 catalytic domain of human neutrophil collagenase (PMNL-CL, MMP-8) using the recently solved model of the Met80-Gly242 form for phasing and subsequently refined it to a final crystallographic R-factor of 18.0% at 2.5 A resolution. The PMNL-CL catalytic domain is a spherical molecule with a flat active site cleft separating a smaller C-terminal subdomain from a bigger N-terminal domain, that harbours two zinc ions, namely a 'structural' and a 'catalytic' zinc, and two calcium ions. The N-terminal segment prior to Pro86, which is disordered in the Met80-Gly242 form, packs against a concave hydrophobic surface made by the C-terminal helix. The N-terminal Phe79 ammonium group makes a salt link with the side chain carboxylate group of the strictly conserved Asp232. Stabilization of the catalytic site might be conferred via strong hydrogen bonds made by the adjacent, likewise strictly conserved Asp233 with the characteristic 'Met-turn', which forms the base of the active site residues.
Structural implications for the role of the N terminus in the 'superactivation' of collagenases. A crystallographic study.,Reinemer P, Grams F, Huber R, Kleine T, Schnierer S, Piper M, Tschesche H, Bode W FEBS Lett. 1994 Jan 31;338(2):227-33. PMID:8307185<ref>PMID:8307185</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1jan" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Matrix metalloproteinase 3D structures|Matrix metalloproteinase 3D structures]]
*[[Matrix metalloproteinase 3D structures|Matrix metalloproteinase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Neutrophil collagenase]]
[[Category: Bode W]]
[[Category: Bode, W]]
[[Category: Grams F]]
[[Category: Grams, F]]
[[Category: Huber R]]
[[Category: Huber, R]]
[[Category: Kleine T]]
[[Category: Kleine, T]]
[[Category: Pieper M]]
[[Category: Pieper, M]]
[[Category: Reinemer P]]
[[Category: Reinemer, P]]
[[Category: Schnierer S]]
[[Category: Schnierer, S]]
[[Category: Tschesche H]]
[[Category: Tschesche, H]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Metalloprotease]]
[[Category: Metzincin]]
[[Category: Zinc-endopeptidase]]

Revision as of 10:50, 3 April 2024

COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (PHE79 FORM)COMPLEX OF PRO-LEU-GLY-HYDROXYLAMINE WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (PHE79 FORM)

Structural highlights

1jan is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MMP8_HUMAN Can degrade fibrillar type I, II, and III collagens.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1jan, resolution 2.50Å

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