File:SDHEnzyme.jpg
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Summary
{Author:}: MismaiStanford Source: PDB protein Data bank, 1P5J.pdb file Date: 17 May 2011 (original upload date) URL: own work, JMol
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Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled GNU Free Documentation License.http://www.gnu.org/copyleft/fdl.htmlGFDLGNU Free Documentation Licensetruetrue |
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Date/Time | Thumbnail | Dimensions | User | Comment | |
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current | 21:08, 17 May 2011 | 458 × 458 (59 KB) | MIsmaiStanford | {Author:}: MismaiStanford Source: PDB protein Data bank, 1P5J.pdb file Date: 17 May 2011 (original upload date) URL: own work, JMol |
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JPEG file comment | JPEG Encoder Copyright 1998, James R. Weeks and BioElectroMech.
# fullName = "jmolApplet0__7301227818243206__"; # documentBase = "http://www.rcsb.org/pdb/explore/jmol.do?structureId=1P5J&bionumber=1%22; # codeBase = "http://www.rcsb.org/pdb/Viewers/jmol-12.0.41/%22;
stateVersion = 1200041; background [x000000]; axis1Color = "[xff0000]"; axis2Color = "[x008000]"; axis3Color = "[x0000ff]"; set ambientPercent 45; set diffusePercent 84; set specular true; set specularPercent 22; set specularPower 40; set specularExponent 6; set zShadePower 1; statusReporting = true; } function _setFileState() { set allowEmbeddedScripts false; set appendNew true; set appletProxy ""; set applySymmetryToBonds false; set autoBond true; set bondRadiusMilliAngstroms 150; set bondTolerance 0.45; set defaultLattice {0.0 0.0 0.0}; set defaultLoadFilter ""; set defaultLoadScript ""; set defaultVDW Auto; set forceAutoBond false; #set defaultDirectory ""; #set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz%22; #set smilesUrlFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True%22; #set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap%22; #set edsUrlCutoff "load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split(' ')[2]"; set legacyAutoBonding false; set minBondDistance 0.4; set minimizationCriterion 0.0010; set minimizationSteps 100; set pdbGetHeader false; set pdbSequential false; set percentVdwAtom 23; set smallMoleculeMaxAtoms 40000; set smartAromatic true; load /*file*/"http://www1.rcsb.org/pdb/files/1P5J.pdb1.gz%22; } function _setVariableState() { set defaultanglelabel "%VALUE %UNITS"; set defaultcolorscheme "jmol"; set defaultdistancelabel "%VALUE %UNITS"; set defaultdrawarrowscale 0.5; set defaultlattice "{0 0 0}"; set defaultloadfilter ""; set defaultloadscript ""; set defaulttorsionlabel "%VALUE %UNITS"; set defaulttranslucent 0.5; set defaultvdw "Auto"; set allowembeddedscripts true; set allowrotateselected false; set appletproxy ""; set applysymmetrytobonds false; set atompicking true; set atomtypes ""; set autobond true; set autofps false; set axes window; set axesmode 0; set axesscale 2.0; set bondmodeor false; set bondradiusmilliangstroms 150; set bondtolerance 0.45; set cartoonbaseedges false; set cartoonrockets false; set chaincasesensitive false; set dataseparator "~~~"; set defaultstructuredssp true; set delaymaximumms 0; set dipolescale 1.0; set disablepopupmenu false; set displaycellparameters true; set dotdensity 3; set dotscale 1; set dotsselectedonly false; set dotsurface true; set dragselected false; set drawhover false; set drawpicking false; set dsspcalculatehydrogenalways true; set dynamicmeasurements false; set ellipsoidarcs false; set ellipsoidaxes false; set ellipsoidaxisdiameter 0.02; set ellipsoidball true; set ellipsoiddotcount 200; set ellipsoiddots false; set ellipsoidfill false; set forceautobond false; set fractionalrelative false; set gestureswipefactor 1.0; set greyscalerendering false; set hbondsangleminimum 90.0; set hbondsbackbone false; set hbondsdistancemaximum 3.25; set hbondsrasmol true; set hbondssolid false; set helixstep 1; set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm%22; set hermitelevel 0; set hidenameinpopup false; set hidenavigationpoint false; set highresolution false; set historylevel 0; set hoverdelay 0.5; set imagestate true; set iskiosk false; set isosurfacepropertysmoothing true; set justifymeasurements false; set loadatomdatatolerance 0.01; set measureallmodels false; set measurementlabels true; set messagestylechime false; set minbonddistance 0.4; set minimizationcriterion 0.0010; set minimizationrefresh true; set minimizationsilent false; set minimizationsteps 100; set monitorenergy false; set multiplebondradiusfactor 0.0; set multiplebondspacing -1.0; set navigatesurface false; set navigationperiodic false; set navigationspeed 5.0; set pdbgetheader false; set pdbsequential false; set percentvdwatom 23; set pickingspinrate 10; set picklabel ""; set pointgroupdistancetolerance 0.2; set pointgrouplineartolerance 8.0; set propertyatomnumbercolumncount 0; set propertyatomnumberfield 0; set propertycolorscheme "roygb"; set propertydatacolumncount 0; set propertydatafield 0; set quaternionframe "p"; set rangeselected false; set ribbonaspectratio 16; set ribbonborder false; set rocketbarrels false; set saveproteinstructurestate true; set selectallmodels true; set selecthetero true; set selecthydrogen true; set sheetsmoothing 1.0; set showhiddenselectionhalos false; set showhydrogens true; set showkeystrokes true; set showmeasurements true; set showmultiplebonds true; set shownavigationpointalways false; set slabbyatom false; set slabbymolecule false; set smallmoleculemaxatoms 40000; set smartaromatic true; set solventprobe false; set solventproberadius 1.2; set ssbondsbackbone false; set stereodegrees -5; set strandcountformeshribbon 7; set strandcountforstrands 5; set strutdefaultradius 0.3; set strutlengthmaximum 7.0; set strutsmultiple false; set strutspacing 6; set testflag1 false; set testflag2 false; set testflag3 false; set testflag4 false; set tracealpha true; set usearcball false; set useminimizationthread true; set usenumberlocalization true; set vectorscale 1.0; set vibrationscale 1.0; set wireframerotation false; set zoomlarge true;
select none; color label none; background label none; set labelOffset 4 4; set labelAlignment left; set labelPointer off; font label 13.0 SansSerif Plain; } function _setModelState() { data "connect_atoms" 54 41 6144 0.0010 -1.039 hbond; 76 189 4096 0.0010 -2.487 hbond; 95 170 4096 0.0010 -2.066 hbond; 95 79 6144 0.0010 -1.07 hbond; 101 90 6144 0.0010 -0.758 hbond; 122 98 10240 0.0010 -1.626 hbond; 128 104 10240 0.0010 -1.815 hbond; 137 112 10240 0.0010 -1.985 hbond; 145 117 10240 0.0010 -1.831 hbond; 150 125 10240 0.0010 -1.8 hbond; 154 125 12288 0.0010 -1.22 hbond; 174 2179 4096 0.0010 -3.616 hbond; 186 79 4096 0.0010 -2.451 hbond; 194 2194 4096 0.0010 -2.069 hbond; 203 64 4096 0.0010 -2.602 hbond; 203 189 6144 0.0010 -0.908 hbond; 211 197 6144 0.0010 -1.854 hbond; 219 2209 4096 0.0010 -0.581 hbond; 225 206 8192 0.0010 -1.449 hbond; 230 214 8192 0.0010 -1.535 hbond; 252 233 8192 0.0010 -1.839 hbond; 262 2216 4096 0.0010 -1.168 hbond; 282 259 8192 0.0010 -1.098 hbond; 290 265 8192 0.0010 -2.351 hbond; 305 276 10240 0.0010 -1.827 hbond; 317 293 10240 0.0010 -1.946 hbond; 327 304 10240 0.0010 -2.307 hbond; 338 308 10240 0.0010 -3.083 hbond; 344 316 10240 0.0010 -2.651 hbond; 353 320 10240 0.0010 -2.221 hbond; 364 330 10240 0.0010 -1.753 hbond; 378 341 10240 0.0010 -2.263 hbond; 383 347 10240 0.0010 -2.232 hbond; 392 356 10240 0.0010 -1.319 hbond; 401 381 8192 0.0010 -0.881 hbond; 405 367 12288 0.0010 -2.606 hbond; 411 918 4096 0.0010 -2.839 hbond; 416 918 4096 0.0010 -1.327 hbond; 426 575 4096 0.0010 -2.693 hbond; 437 936 4096 0.0010 -2.95 hbond; 444 587 4096 0.0010 -1.869 hbond; 488 470 10240 0.0010 -2.134 hbond; 496 474 10240 0.0010 -2.874 hbond; 501 482 10240 0.0010 -2.723 hbond; 506 487 10240 0.0010 -3.277 hbond; 511 491 10240 0.0010 -2.151 hbond; 523 499 10240 0.0010 -2.635 hbond; 528 504 10240 0.0010 -2.438 hbond; 533 509 10240 0.0010 -2.061 hbond; 544 514 10240 0.0010 -2.604 hbond; 553 526 10240 0.0010 -1.953 hbond; 561 531 10240 0.0010 -0.945 hbond; 561 536 8192 0.0010 -0.811 hbond; 565 531 12288 0.0010 -2.243 hbond; 584 429 4096 0.0010 -3.474 hbond; 591 739 4096 0.0010 -3.824 hbond; 599 447 4096 0.0010 -2.431 hbond; 606 752 4096 0.0010 -2.636 hbond; 620 775 4096 0.0010 -1.12 hbond; 631 616 8192 0.0010 -0.895 hbond; 665 641 10240 0.0010 -1.917 hbond; 673 648 10240 0.0010 -1.671 hbond; 682 653 10240 0.0010 -2.632 hbond; 693 661 10240 0.0010 -1.907 hbond; 701 668 10240 0.0010 -2.464 hbond; 710 676 10240 0.0010 -1.996 hbond; 718 685 10240 0.0010 -0.999 hbond; 718 696 8192 0.0010 -0.729 hbond; 727 704 8192 0.0010 -1.603 hbond; 731 696 12288 0.0010 -1.129 hbond; 736 582 4096 0.0010 -2.825 hbond; 749 594 4096 0.0010 -2.886 hbond; 765 609 4096 0.0010 -2.599 hbond; 809 788 8192 0.0010 -1.123 hbond; 818 788 10240 0.0010 -1.222 hbond; 823 796 10240 0.0010 -1.664 hbond; 834 804 10240 0.0010 -0.795 hbond; 843 812 10240 0.0010 -2.338 hbond; 851 821 10240 0.0010 -2.473 hbond; 856 826 10240 0.0010 -2.707 hbond; 865 837 10240 0.0010 -1.632 hbond; 870 846 10240 0.0010 -2.515 hbond; 878 854 10240 0.0010 -1.857 hbond; 883 859 10240 0.0010 -1.581 hbond; 892 868 10240 0.0010 -3.125 hbond; 900 873 10240 0.0010 -0.592 hbond; 919 903 8192 0.0010 -1.891 hbond; 933 419 4096 0.0010 -2.459 hbond; 952 440 4096 0.0010 -2.863 hbond; 993 977 6144 0.0010 -1.843 hbond; 1016 996 8192 0.0010 -0.81 hbond; 1024 996 10240 0.0010 -1.916 hbond; 1038 1004 10240 0.0010 -2.282 hbond; 1047 1011 10240 0.0010 -2.205 hbond; 1051 1019 10240 0.0010 -2.317 hbond; 1061 1027 10240 0.0010 -2.112 hbond; 1066 1050 8192 0.0010 -1.158 hbond; 1072 1054 8192 0.0010 -2.711 hbond; 1080 1064 8192 0.0010 -1.23 hbond; 1087 1064 10240 0.0010 -1.342 hbond; 1096 1069 10240 0.0010 -1.893 hbond; 1105 1075 10240 0.0010 -1.519 hbond; 1113 1083 10240 0.0010 -2.528 hbond; 1122 1090 10240 0.0010 -1.572 hbond; 1131 1099 10240 0.0010 -2.252 hbond; 1138 1108 10240 0.0010 -2.151 hbond; 1185 2173 4096 0.0010 -0.612 hbond; 1189 2173 4096 0.0010 -0.968 hbond; 1194 1369 4096 0.0010 -2.732 hbond; 1202 2187 4096 0.0010 -3.005 hbond; 1207 1383 4096 0.0010 -2.198 hbond; 1221 1396 4096 0.0010 -2.148 hbond; 1260 1239 10240 0.0010 -2.699 hbond; 1266 1243 10240 0.0010 -2.368 hbond; 1270 1247 10240 0.0010 -3.158 hbond; 1277 1255 10240 0.0010 -1.394 hbond; 1284 1263 10240 0.0010 -2.241 hbond; 1293 1269 10240 0.0010 -2.628 hbond; 1297 1273 10240 0.0010 -2.266 hbond; 1305 1280 10240 0.0010 -2.479 hbond; 1314 1287 10240 0.0010 -2.328 hbond; 1323 1296 10240 0.0010 -1.155 hbond; 1329 1308 8192 0.0010 -1.061 hbond; 1333 1300 12288 0.0010 -2.464 hbond; 1359 1336 8192 0.0010 -2.28 hbond; 1373 1741 4096 0.0010 -2.618 hbond; 1380 1197 4096 0.0010 -4.112 hbond; 1388 1756 4096 0.0010 -1.943 hbond; 1388 1376 6144 0.0010 -0.959 hbond; 1393 1210 4096 0.0010 -3.209 hbond; 1393 1383 6144 0.0010 -0.931 hbond; 1401 1773 4096 0.0010 -2.029 hbond; 1417 1789 4096 0.0010 -2.469 hbond; 1432 1413 8192 0.0010 -1.881 hbond; 1447 1435 6144 0.0010 -1.958 hbond; 1474 1440 10240 0.0010 -1.742 hbond; 1479 1450 10240 0.0010 -1.62 hbond; 1484 1456 10240 0.0010 -2.671 hbond; 1491 1467 10240 0.0010 -2.354 hbond; 1498 1477 10240 0.0010 -1.516 hbond; 1503 1482 10240 0.0010 -1.86 hbond; 1507 1482 12288 0.0010 -1.18 hbond; 1537 1630 4096 0.0010 -2.618 hbond; 1569 1431 4096 0.0010 -1.756 hbond; 1576 1431 4096 0.0010 -1.471 hbond; 1594 1585 6144 0.0010 -2.101 hbond; 1608 1592 8192 0.0010 -2.118 hbond; 1616 1597 8192 0.0010 -1.167 hbond; 1616 1592 10240 0.0010 -0.781 hbond; 1620 1611 6144 0.0010 -2.741 hbond; 1650 1235 4096 0.0010 -2.709 hbond; 1674 1653 10240 0.0010 -1.329 hbond; 1682 1657 10240 0.0010 -1.933 hbond; 1691 1663 10240 0.0010 -2.175 hbond; 1699 1672 10240 0.0010 -0.991 hbond; 1710 1685 8192 0.0010 -0.848 hbond; 1719 1685 10240 0.0010 -0.554 hbond; 1728 1694 10240 0.0010 -0.794 hbond; 1745 1731 6144 0.0010 -1.027 hbond; 1753 1376 4096 0.0010 -2.884 hbond; 1770 1391 4096 0.0010 -2.327 hbond; 1786 1404 4096 0.0010 -2.466 hbond; 1826 1797 10240 0.0010 -1.733 hbond; 1831 1803 10240 0.0010 -2.817 hbond; 1838 1811 10240 0.0010 -2.583 hbond; 1843 1820 10240 0.0010 -1.122 hbond; 1848 1829 10240 0.0010 -1.512 hbond; 1856 1834 10240 0.0010 -1.938 hbond; 1865 1841 10240 0.0010 -2.501 hbond; 1874 1846 10240 0.0010 -2.585 hbond; 1885 1851 10240 0.0010 -1.992 hbond; 1892 1859 10240 0.0010 -1.049 hbond; 1900 1868 10240 0.0010 -1.773 hbond; 1908 1877 10240 0.0010 -1.885 hbond; 1917 1877 12288 0.0010 -0.863 hbond; 1949 2222 4096 0.0010 -2.133 hbond; 1970 1952 8192 0.0010 -1.156 hbond; 1976 1952 10240 0.0010 -2.219 hbond; 1980 1961 10240 0.0010 -2.115 hbond; 1985 1968 10240 0.0010 -1.039 hbond; 1990 1973 10240 0.0010 -2.657 hbond; 1998 1979 10240 0.0010 -1.933 hbond; 2003 1988 8192 0.0010 -1.927 hbond; 2008 1993 8192 0.0010 -1.805 hbond; 2015 1993 10240 0.0010 -1.678 hbond; 2027 2001 10240 0.0010 -2.21 hbond; 2033 2011 8192 0.0010 -2.119 hbond; 2050 2006 4096 0.0010 -1.546 hbond; 2067 2036 10240 0.0010 -1.716 hbond; 2076 2046 10240 0.0010 -2.256 hbond; 2084 2053 10240 0.0010 -2.337 hbond; 2093 2061 10240 0.0010 -2.616 hbond; 2101 2070 10240 0.0010 -1.797 hbond; 2110 2087 8192 0.0010 -0.98 hbond; 2114 2079 12288 0.0010 -2.105 hbond; 2122 2079 4096 0.0010 -1.664 hbond; 2176 164 4096 0.0010 -2.931 hbond; 2184 1192 4096 0.0010 -2.774 hbond; 2191 177 4096 0.0010 -2.805 hbond; 2198 1205 4096 0.0010 -3.002 hbond; 2206 197 4096 0.0010 -2.014 hbond; 2206 2194 6144 0.0010 -1.061 hbond; 2213 2201 6144 0.0010 -1.889 hbond; 2223 255 4096 0.0010 -2.565 hbond; 2241 2230 6144 0.0010 -1.423 hbond; 2277 2252 10240 0.0010 -2.511 hbond; 2285 2258 10240 0.0010 -2.164 hbond; 2296 2266 10240 0.0010 -2.593 hbond; 2301 2271 10240 0.0010 -3.362 hbond; 2309 2280 10240 0.0010 -2.925 hbond; 2318 2288 10240 0.0010 -2.997 hbond; 2327 2299 10240 0.0010 -3.201 hbond; 2336 2304 10240 0.0010 -1.399 hbond; 2344 2321 8192 0.0010 -1.45 hbond; 2344 2312 10240 0.0010 -0.902 hbond; 2348 2312 12288 0.0010 -2.284 hbond; end "connect_atoms"; select ({0:100}); color atoms opaque [x0000ff]; select ({1428:1515}); color atoms opaque [x00ff20]; select ({572:657}); color atoms opaque [x00c0ff]; select ({2386:2398}); color atoms opaque [xfff000]; select ({851:951}); color atoms opaque [x00ffe0]; select ({2277:2355 2371 2372}); color atoms opaque [xf0f000]; select ({2450:2462}); color atoms opaque [xff6000]; select ({1608:1698}); color atoms opaque [x20ff00]; select ({1699:1807}); color atoms opaque [x40ff00]; select ({1516:1607}); color atoms opaque [x00ff00]; select ({1808:1907}); color atoms opaque [x60ff00]; select ({1908:1997}); color atoms opaque [x80ff00]; select ({2373:2385}); color atoms opaque [xffff00]; select ({2476:2488}); color atoms opaque [xff2000]; select ({1169:1243}); color atoms opaque [x00ff80]; select ({952:1060}); color atoms opaque [x00ffc0]; select ({290:400}); color atoms opaque [x0060ff]; select ({2399:2411}); color atoms opaque [xffe000]; select ({1998:2092}); color atoms opaque [xa0ff00]; select ({749:850}); color atoms opaque [x00ffff]; select ({2093:2190}); color atoms opaque [xc0ff00]; select ({2191:2276}); color atoms opaque [xe0ff00]; select ({101:193}); color atoms opaque [x0020ff]; select ({2424:2436}); color atoms opaque [xffa000]; select ({658:748}); color atoms opaque [x00e0ff]; select ({1244:1332}); color atoms opaque [x00ff60]; select ({484:571}); color atoms opaque [x00a0ff]; select ({1061:1168}); color atoms opaque [x00ffa0]; select ({2437:2449}); color atoms opaque [xff8000]; select ({2463:2475}); color atoms opaque [xff4000]; select ({1333:1427}); color atoms opaque [x00ff40]; select ({401:483}); color atoms opaque [x0080ff]; select ({2356:2370}); Spacefill 0.5; select ({2489:2501}); color atoms opaque [xff0000]; select ({194:289}); color atoms opaque [x0040ff]; select ({2412:2423}); color atoms opaque [xffc000]; select ({0:2355 2371:2501}); Spacefill 0.0; select BONDS ({2404:2409 2411:2419}); wireframe 0.16; select BONDS ({2420:2635}); wireframe on; color bonds opaque [xff00ff]; select BONDS ({0:2403 2410}); wireframe 0.0; measures delete; select *; set measures angstroms; font measures 15.0 SansSerif Plain; select ({0:2355}); Cartoon on; select ({401:483}); color Cartoon opaque [x0080ff]; select ({1998:2092}); color Cartoon opaque [xa0ff00]; select ({0:100}); color Cartoon opaque [x0000ff]; select ({1908:1997}); color Cartoon opaque [x80ff00]; select ({1516:1607}); color Cartoon opaque [x00ff00]; select ({1428:1515}); color Cartoon opaque [x00ff20]; select ({1061:1168}); color Cartoon opaque [x00ffa0]; select ({101:193}); color Cartoon opaque [x0020ff]; select ({484:571}); color Cartoon opaque [x00a0ff]; select ({2093:2190}); color Cartoon opaque [xc0ff00]; select ({952:1060}); color Cartoon opaque [x00ffc0]; select ({1333:1427}); color Cartoon opaque [x00ff40]; select ({749:850}); color Cartoon opaque [x00ffff]; select ({851:951}); color Cartoon opaque [x00ffe0]; select ({1244:1332}); color Cartoon opaque [x00ff60]; select ({1608:1698}); color Cartoon opaque [x20ff00]; select ({194:289}); color Cartoon opaque [x0040ff]; select ({572:657}); color Cartoon opaque [x00c0ff]; select ({1169:1243}); color Cartoon opaque [x00ff80]; select ({2277:2355}); color Cartoon opaque [xf0f000]; select ({2191:2276}); color Cartoon opaque [xe0ff00]; select ({290:400}); color Cartoon opaque [x0060ff]; select ({658:748}); color Cartoon opaque [x00e0ff]; select ({1808:1907}); color Cartoon opaque [x60ff00]; select ({1699:1807}); color Cartoon opaque [x40ff00]; boundBox off; font boundBox 14.0 SansSerif Plain; boundBox off; unitcell off; font unitcell 14.0 SansSerif Plain; unitcell off; frank on; font frank 16.0 SansSerif Bold; select *; } function _setPerspectiveState() { set perspectiveModel 11; set scaleAngstromsPerInch 0.0; set perspectiveDepth true; set visualRange 5.0; set cameraDepth 3.0; boundbox corners {-40.987003 14.127003 -23.125} {6.6590004 62.577 40.076} # volume = 145896.27; center {-17.164001 38.352 8.4755}; moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {-17.164001 38.352 8.4755} 35.811337 {0.0 0.0 0.0} 0.0 0.0 0.0; save orientation "default"; moveto 0.0 { -423 880 -218 36.68} 100.0 0.0 0.0 {-17.164001 38.352 8.4755} 35.811337 {0.0 0.0 0.0} 10.40744 57.42628 0.0;; slab 100;depth 0; set spinX 0; set spinY 30; set spinZ 0; set spinFps 30; set navX 0; set navY 0; set navZ 0; set navFps 10; } function _setSelectionState() { select ({0:2501}); set hideNotSelected false; } function _setState() { initialize; set refreshing false; _setWindowState; _setFileState; _setVariableState; _setModelState; _setPerspectiveState; _setSelectionState; set refreshing true; set antialiasDisplay true; set antialiasTranslucent true; set antialiasImages true; } _setState;
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