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.


1ic6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:46, 3 April 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ic6.jpg|left|200px]]
 
-
{{Structure
+
==STRUCTURE OF A SERINE PROTEASE PROTEINASE K FROM TRITIRACHIUM ALBUM LIMBER AT 0.98 A RESOLUTION==
-
|PDB= 1ic6 |SIZE=350|CAPTION= <scene name='initialview01'>1ic6</scene>, resolution 0.98&Aring;
+
<StructureSection load='1ic6' size='340' side='right'caption='[[1ic6]], [[Resolution|resolution]] 0.98&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>
+
<table><tr><td colspan='2'>[[1ic6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Parengyodontium_album Parengyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IC6 FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidase_K Peptidase K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] </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]] 0.98&#8491;</td></tr>
-
|GENE=
+
<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=NO3:NITRATE+ION'>NO3</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=1ic6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ic6 OCA], [https://pdbe.org/1ic6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ic6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ic6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ic6 ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ic6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ic6 OCA], [http://www.ebi.ac.uk/pdbsum/1ic6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ic6 RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/PRTK_PARAQ PRTK_PARAQ] Hydrolyzes keratin at aromatic and hydrophobic residues.
 +
== 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/ic/1ic6_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=1ic6 ConSurf].
 +
<div style="clear:both"></div>
-
'''STRUCTURE OF A SERINE PROTEASE PROTEINASE K FROM TRITIRACHIUM ALBUM LIMBER AT 0.98 A RESOLUTION'''
+
==See Also==
-
 
+
*[[Proteinase 3D structures|Proteinase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
X-ray diffraction data at atomic resolution to 0.98 A with 136 380 observed unique reflections were collected using a high quality proteinase K crystals grown under microgravity conditions and cryocooled. The structure has been refined anisotropically with REFMAC and SHELX-97 with R-factors of 11.4 and 12.8%, and R(free)-factors of 12.4 and 13.5%, respectively. The refined model coordinates have an overall rms shifts of 0.23 A relative to the same structure determined at room temperature at 1.5 A resolution. Several regions of the main chain and the side chains, which were not observed earlier have been seen more clearly. For example, amino acid 207, which was reported earlier as Ser has been clearly identified as Asp. Furthermore, side-chain disorders of 8 of 279 residues in the polypeptide have been identified. Hydrogen atoms appear as significant peaks in the F(o) - F(c) difference electron density map accounting for an estimated 46% of all hydrogen atoms at 2sigma level. Furthermore, the carbon, nitrogen, and oxygen atoms can be differentiated clearly in the electron density maps. Hydrogen bonds are clearly identified in the serine protease catalytic triad (Ser-His-Asp). Furthermore, electron density is observed for an unusual, short hydrogen bond between aspartic acid and histidine in the catalytic triad. The short hydrogen bond, designated "catalytic hydrogen bond", occurs as part of an elaborate hydrogen bond network, involving Asp of the catalytic triad. Though unusual, these features seem to be conserved in other serine proteases. Finally there are clear electron density peaks for the hydrogen atoms associated with the Ogamma of Ser 224 and Ndelta1 of His 69.
+
[[Category: Large Structures]]
-
 
+
[[Category: Parengyodontium album]]
-
==About this Structure==
+
[[Category: Betzel C]]
-
1IC6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Engyodontium_album Engyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IC6 OCA].
+
[[Category: Eschenburg S]]
-
 
+
[[Category: Gourinath S]]
-
==Reference==
+
[[Category: Kaur P]]
-
Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 A resolution., Betzel C, Gourinath S, Kumar P, Kaur P, Perbandt M, Eschenburg S, Singh TP, Biochemistry. 2001 Mar 13;40(10):3080-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11258922 11258922]
+
[[Category: Kumar P]]
-
[[Category: Engyodontium album]]
+
[[Category: Perbandt M]]
-
[[Category: Peptidase K]]
+
[[Category: Singh TP]]
-
[[Category: Single protein]]
+
-
[[Category: Betzel, C.]]
+
-
[[Category: Eschenburg, S.]]
+
-
[[Category: Gourinath, S.]]
+
-
[[Category: Kaur, P.]]
+
-
[[Category: Kumar, P.]]
+
-
[[Category: Perbandt, M.]]
+
-
[[Category: Singh, T P.]]
+
-
[[Category: proteinase k]]
+
-
[[Category: serine protease]]
+
-
[[Category: structure]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:17:39 2008''
+

Current revision

STRUCTURE OF A SERINE PROTEASE PROTEINASE K FROM TRITIRACHIUM ALBUM LIMBER AT 0.98 A RESOLUTION

PDB ID 1ic6

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/1ic6"
Personal tools