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| <applet load='Dnac_from_2ggz_a.pdb' size='500' frame='true' align='right' | | <StructureSection load='' size='350' side='right' caption='' scene=''> |
| scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6' /> | |
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| The following sequence was provided for DnaC from E. coli:
| | *1 <scene name='31/319439/Surface_test/1'>Surface test 1</scene>: simple surface on chain A of 1d66. Colored translucent green. This surface was generated with the '''representations''' tab of the SAT. |
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| <tt>
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| MKNVGDLMQR LQKMMPAHIK PAFKTGEELL AWQKEQGAIR SAALERENRA
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| <br>
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| MKMQ<b>RTFNRS GIRPLHQNCS FENYRVECEG QMNALSKARQ YVEEFDGNIA
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| <br>
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| SFIFSGKPGT GKNHLAAAIC NELLLRGKSV LIITVADIMS AMKDTFRNSG
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| <br>
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| TSEEQLLNDL SNVDLLVIDE IGVQTESKYE KVIINQIVDR RSSSKRPTGM
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| <br>
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| LTNSNMEEMT KLLGERVMDR MRLGNSLWVI FNWDSYR</b>SRV TGKEY
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| </tt>
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| This sequence was submitted to Swiss Model, which [http://tinyurl.com/4nek2q generated the homology model] shown here (<scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/6'>restore initial scene</scene>) using [[2qgz]] chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237, shown in boldface in the above sequence.
| | *2 <scene name='31/319439/6zgi_translucen_backbone/1'>6zgi as translucent backbone, chain colors</scene> (no isosurfaces). After clicking this standard SAT-generated green link, then |
| | <jmol> |
| | <jmolButton> |
| | <script> |
| | isosurface delete; isosurface "http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl"; |
| | </script> |
| | <text>Load isosurface cavities</text> |
| | </jmolButton> |
| | </jmol> |
| | (From uploaded file http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl -- see [[Image:6zgi-cavities.jvxl]]) |
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| Swiss Model has apparently used the [[temperature value]] field in the PDB file to indicate regions that are highly unreliable, namely the regions that are <font color="red"><b>red</b></font> when the model is <scene name='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/4'>colored by temperature</scene>. These regions are shown as '''translucent white''' in the initial scene (using the Jmol command <i>select temperature >50</i>).
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| In order to find specific residues, or see other aspects of this homology model, please use:
| | *3 <jmol> |
| | <jmolButton> |
| | <script> |
| | load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj"; |
| | </script> |
| | <text>Load .PNGJ file</text> |
| | </jmolButton> |
| | </jmol> |
| | (From uploaded file http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj -- see [http://proteopedia.org/wiki/index.php/Image:6zgi-cavities.pngj Image:6zgi-cavities.png]) |
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| [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=http%3A//proteopedia.org/wiki/images/3/3e/Dnac_from_2ggz_a.pdb View DnaC Homology Model in FirstGlance in Jmol]
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| The template was <scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>2qgz</scene>. The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms).
| | *4 <jmol> |
| | <jmolLink> |
| | <script> |
| | load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj"; |
| | </script> |
| | <text>Green link loading uploaded PNGJ file</text> |
| | </jmolLink> |
| | </jmol>. SAT not involved. PNGJ file generated externally in the [[Jmol/Application|Jmol Java application]], then uploaded to Proteopedia as for the previous item above. |
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| The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). These gaps, which occur between the residues marked /\ below, were apparently ignored in making the model, which has a continuous main chain.
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| Alignment produced by Swiss Model, used in making the 3D model:
| | *5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.) |
| <pre>
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| TARGET 55 R TFNRSGIRPL HQNCSFENYR VECEGQMNAL SKARQYVEEF
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| 2qgzA 100 qkqaais--e riqlvslpks yrhihlsdid vnnasrmeaf saildfveqy
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| TARGET sssss h h hhhhhhh hhhhhhhhh
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| 2qgzA hhh h sss h h hhhhhhh hhhhhhhhh
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| TARGET 96 DGN-IASFIF SGKPGTGKNH LAAAICNELL L-RGKSVLII TVADIMSAMK
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| 2qgzA 148 psaeqkglyl ygdmgigksy llaamahels ekkgvsttll hfpsfaidvk
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| TARGET ssss ss hhh hhhhhhhhhh h h ssss sshhhhhhh
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| 2qgzA ssss ss hhh hhhhhhhhhh hh ssss sshhhhhhh
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| | Tested in Firefox (current version) on macOS Mojave, mid-2014 MacBook Pro, 2.2 GHz Intel Core i7. |
| TARGET 144 DTFRNSGTSE EQLLNDLSNV DLLVIDEIGV QTESKYEKVI INQIVDRRSS
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| 2qgzA 198 naiske---- --eidavknv pvlilddiga vrde-----v lqvilqyrml
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| /\ / \
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| TARGET hhh ssssss hhhhhhhhhh
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| 2qgzA hh h ssssss hhhhhhhhhh
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| | *6 <scene name='31/319439/6zgi_cavities/1'>Cavities in coronavirus spike protein 6zgi</scene>. It took 8.5 min to generate the cavity isosurfaces after I entered the command "isosurface minset 100 interior cavity 3.0 10.0" into the command slot in the SAT. (This command takes ~45 sec in the Jmol Java app which is therefore 11-fold faster for this operation.) After clicking this green link, I waited 11 min and the scene still did not appear. So I think the isosurfaces are being generated again when the green link is clicked. |
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| TARGET 194 SKRPTGMLTN SNMEEMTKLL ---GERVMDR MRLGNSLWVI FNWDSYR
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| 2qgzA 247 eelptfftsn ysfadlerkw awqakrvmer vr-ylarefh leganrr-
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| /\
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| TARGET h ssssss hhhhh hhhh hh ssssss s
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| 2qgzA h ssssss hhhh hhhh hh hh ssss s
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| </pre>
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| Below is the sequence with ATOM records (coordinates) from 2QGZ, numbered 100-300, showing the gaps as "...". This sequence listing was used to locate the positions marked /\ above.
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| <pre>
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| 1 .......... .......... .......... .......... ..........
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| 51 .......... .......... .......... .......... .........Q
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| 101 KQAAISERIQ LVSLPKSYRH IHLSDIDVNN ASRMEAFSAI LDFVEQYPSA
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| 151 EQKGLYLYGD MGIGKSYLLA AMAHELSEKK GVSTTLLHFP SFAIDVKNAI
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| 201 S....KEEID AVKNVPVLIL DDIGA..... .VRDEVLQVI LQYRMLEELP
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| 251 TFFTSNYSFA DLERKWA... .....WQAKR VMERVRYLAR EFHLEGANRR
| | </StructureSection> |
| </pre> | |
| (Copied from Protein Explorer's sequence display.)
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