1khq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:35, 6 November 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1khq.gif|left|200px]]
 
-
{{Structure
+
==ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX==
-
|PDB= 1khq |SIZE=350|CAPTION= <scene name='initialview01'>1khq</scene>, resolution 1.6&Aring;
+
<StructureSection load='1khq' size='340' side='right'caption='[[1khq]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=GLM:1-AMINO-PROPAN-2-ONE'>GLM</scene>
+
<table><tr><td colspan='2'>[[1khq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KHQ FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0HQ:DIAZOMETHANE'>0HQ</scene>, <scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1khq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1khq OCA], [https://pdbe.org/1khq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1khq RCSB], [https://www.ebi.ac.uk/pdbsum/1khq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1khq ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1pad|1PAD]], [[5pad|5PAD]], [[6pad|6PAD]], [[9pap|9PAP]], [[1ppn|1PPN]], [[2pad|2PAD]], [[1pe6|1PE6]], [[1pip|1PIP]], [[1ppp|1PPP]], [[1ppd|1PPD]], [[1pop|1POP]], [[1stf|1STF]], [[1cvz|1CVZ]], [[1khp|1KHP]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1khq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1khq OCA], [http://www.ebi.ac.uk/pdbsum/1khq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1khq RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/PAPA1_CARPA PAPA1_CARPA]
 +
== 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/kh/1khq_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1khq ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The three-dimensional structure of two polymorphs of a ZLFG-CH2-papain covalent complex has been determined by X-ray crystallography. The structures indicate that: (i) the methylene carbon atom of the inhibitor is covalently bound to the Sgamma atom of Cys25 of papain; (ii) the hydrophobic S2 pocket formed by Pro68, Val133, Val157, and Asp158 is occupied by the inhibitor's phenylalanyl P2 side chain; (iii) extensive hydrogen bonding and hydrophobic interactions are responsible for the interaction of the inhibitor with the enzyme. Comparison with similar structures suggests that in covalent complexes preservation of main chain-main chain interactions between the enzyme and the inhibitor may have higher priority than the P-S interactions.
-
'''ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX'''
+
Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor.,Janowski R, Kozak M, Jankowska E, Grzonka Z, Jaskolski M J Pept Res. 2004 Oct;64(4):141-50. PMID:15357669<ref>PMID:15357669</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1khq" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
The three-dimensional structure of two polymorphs of a ZLFG-CH2-papain covalent complex has been determined by X-ray crystallography. The structures indicate that: (i) the methylene carbon atom of the inhibitor is covalently bound to the Sgamma atom of Cys25 of papain; (ii) the hydrophobic S2 pocket formed by Pro68, Val133, Val157, and Asp158 is occupied by the inhibitor's phenylalanyl P2 side chain; (iii) extensive hydrogen bonding and hydrophobic interactions are responsible for the interaction of the inhibitor with the enzyme. Comparison with similar structures suggests that in covalent complexes preservation of main chain-main chain interactions between the enzyme and the inhibitor may have higher priority than the P-S interactions.
+
*[[Papain|Papain]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1KHQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHQ OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
-
Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor., Janowski R, Kozak M, Jankowska E, Grzonka Z, Jaskolski M, J Pept Res. 2004 Oct;64(4):141-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15357669 15357669]
+
[[Category: Carica papaya]]
[[Category: Carica papaya]]
-
[[Category: Papain]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Grzonka Z]]
-
[[Category: Grzonka, Z.]]
+
[[Category: Jankowska E]]
-
[[Category: Jankowska, E.]]
+
[[Category: Janowski R]]
-
[[Category: Janowski, R.]]
+
[[Category: Jaskolski M]]
-
[[Category: Jaskolski, M.]]
+
[[Category: Kozak M]]
-
[[Category: Kozak, M.]]
+
-
[[Category: diazomethylketone inhibitor]]
+
-
[[Category: irreversible inhibitor]]
+
-
[[Category: protease inhibitor]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:48:45 2008''
+

Current revision

ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX

PDB ID 1khq

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/1khq"
Personal tools