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1npz

From Proteopedia

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Crystal structures of Cathepsin S inhibitor complexes

Structural highlights

1npz 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 2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CATS_HUMAN Thiol protease. Key protease responsible for the removal of the invariant chain from MHC class II molecules. The bond-specificity of this proteinase is in part similar to the specificities of cathepsin L and cathepsin N.

Evolutionary Conservation

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

Publication Abstract from PubMed

Cathepsin S, a lysosomal cysteine protease of the papain superfamily, has been implicated in the preparation of MHC class II alphabeta-heterodimers for antigen presentation to CD4+ T lymphocytes and is considered a potential target for autoimmune-disease therapy. Selective inhibition of this enzyme may be therapeutically useful for attenuating the hyperimmune responses in a number of disorders. We determined the three-dimensional crystal structures of human cathepsin S in complex with potent covalent inhibitors, the aldehyde inhibitor 4-morpholinecarbonyl-Phe-(S-benzyl)Cys-Psi(CH=O), and the vinyl sulfone irreversible inhibitor 4-morpholinecarbonyl-Leu-Hph-Psi(CH=CH-SO(2)-phenyl) at resolutions of 1.8 and 2.0 A, respectively. In the structure of the cathepsin S-aldehyde complex, the tetrahedral thiohemiacetal adduct favors the S-configuration, in which the oxygen atom interacts with the imidazole group of the active site His164 rather than with the oxyanion hole. The present structures provide a detailed map of noncovalent intermolecular interactions established in the substrate-binding subsites S3 to S1' of cathepsin S. In the S2 pocket, which is the binding affinity hot spot of cathepsin S, the Phe211 side chain can assume two stable conformations that accommodate either the P2-Leu or a bulkier P2-Phe side chain. This structural plasticity of the S2 pocket in cathepsin S explains the selective inhibition of cathepsin S over cathepsin K afforded by inhibitors with the P2-Phe side chain. Comparison with the structures of cathepsins K, V, and L allows delineation of local intermolecular contacts that are unique to cathepsin S.

Specificity determinants of human cathepsin s revealed by crystal structures of complexes.,Pauly TA, Sulea T, Ammirati M, Sivaraman J, Danley DE, Griffor MC, Kamath AV, Wang IK, Laird ER, Seddon AP, Menard R, Cygler M, Rath VL Biochemistry. 2003 Mar 25;42(11):3203-13. PMID:12641451^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pauly TA, Sulea T, Ammirati M, Sivaraman J, Danley DE, Griffor MC, Kamath AV, Wang IK, Laird ER, Seddon AP, Menard R, Cygler M, Rath VL. Specificity determinants of human cathepsin s revealed by crystal structures of complexes. Biochemistry. 2003 Mar 25;42(11):3203-13. PMID:12641451 doi:10.1021/bi027308i

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1npz"

@@ Line 1: / Line 1: @@
 ==Crystal structures of Cathepsin S inhibitor complexes==
-<StructureSection load='1npz' size='340' side='right' caption='[[1npz]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1npz' size='340' side='right'caption='[[1npz]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1npz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NPZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1npz]] 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=1NPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NPZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C1P:N~2~-(MORPHOLIN-4-YLCARBONYL)-N-[(3S)-1-PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]-L-LEUCINAMIDE'>C1P</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nqc|1nqc]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C1P:N~2~-(MORPHOLIN-4-YLCARBONYL)-N-[(3S)-1-PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]-L-LEUCINAMIDE'>C1P</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cathepsin_S Cathepsin S], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.27 3.4.22.27] </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=1npz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1npz OCA], [https://pdbe.org/1npz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1npz RCSB], [https://www.ebi.ac.uk/pdbsum/1npz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1npz ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1npz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1npz OCA], [http://pdbe.org/1npz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1npz RCSB], [http://www.ebi.ac.uk/pdbsum/1npz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1npz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CATS_HUMAN CATS_HUMAN]] Thiol protease. Key protease responsible for the removal of the invariant chain from MHC class II molecules. The bond-specificity of this proteinase is in part similar to the specificities of cathepsin L and cathepsin N.
+[https://www.uniprot.org/uniprot/CATS_HUMAN CATS_HUMAN] Thiol protease. Key protease responsible for the removal of the invariant chain from MHC class II molecules. The bond-specificity of this proteinase is in part similar to the specificities of cathepsin L and cathepsin N.
 == 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/np/1npz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/np/1npz_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 29: @@
 </div>
 <div class="pdbe-citations 1npz" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cathepsin 3D structures|Cathepsin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cathepsin S]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
+[[Category: Large Structures]]
-[[Category: Ammirati, M]]
+[[Category: Ammirati M]]
-[[Category: Cygler, M]]
+[[Category: Cygler M]]
-[[Category: Danley, D E]]
+[[Category: Danley DE]]
-[[Category: Griffor, M C]]
+[[Category: Griffor MC]]
-[[Category: Kamath, A V]]
+[[Category: Kamath AV]]
-[[Category: Laird, E R]]
+[[Category: Laird ER]]
-[[Category: Menard, R]]
+[[Category: Menard R]]
-[[Category: Pauly, T A]]
+[[Category: Pauly TA]]
-[[Category: Rath, V L]]
+[[Category: Rath VL]]
-[[Category: Seddon, A P]]
+[[Category: Seddon AP]]
-[[Category: Sivaraman, J]]
+[[Category: Sivaraman J]]
-[[Category: Sulea, T]]
+[[Category: Sulea T]]
-[[Category: Wang, I K]]
+[[Category: Wang IK]]
-[[Category: Antigen presentation]]
-[[Category: Binding specificity]]
-[[Category: Cysteine protease]]
-[[Category: Hydrolase]]
-[[Category: Inhibitor complex]]
-[[Category: Structural plasticity]]
-[[Category: Structure-based design]]

1npz

From Proteopedia

Current revision

Crystal structures of Cathepsin S inhibitor complexes

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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