Literature reference for the structure:
Dyda, Furey, Swaminathan, Sax, Farrenkopf, Jordan, Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution, Biochemistry 32 pp. 6165 (1993)

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Presentation by Craig Martin
Last updated: October 19, 2004

(JmolShell last updated: Apr 2, 2013)

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This JmolShell presentation made possible by Jmol, an open-source project, using a set of JavaScript functions provided in the library Jmol.js

Developed using JmolShell, by Craig Martin, cmartin@chem.umass.edu, Department of Chemistry, University of Massachusetts, Amherst, MA

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Molecule info:

Please wait...

Enter a multi-line Jmol script here (Help):

      Insert Jmol command - Current view Sticks & Labels

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This JmolShell presentation made possible by Jmol, an open-source project. Scripting commands follow those of Rasmol/CHIME. (see also the Jmol Wiki).

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The Jmol mouse gestures are designed to function with single-button mice on the Mac. All references to 'left' get translated to 'only'

rotate X and Y axes	left drag
zoom + rotate Z axis	shift left drag OR middle button drag
rotate Z axis only	shift right drag
translate X and Y axes	shift double left drag OR double middle drag
reset to center	shift double left click OR double middle click
wheel - zoom	a wheel is also a middle button if clicked/dragged
popup menu	right click OR ctrl left click

To measure distances and angles

Double click, optionally single click 0, 1, or 2 times, Double click

After your first double-click the cursor will change and then you can'hover' over several different atoms to get different distances.

Move outside the applet to cancel the measurement.

For a distance measurment:

double click to drop an anchor
double click on the destination

For an angle measurement:

double click to drop an anchor
single click on an intermediate point
double click on the final point

For a torsion measurement:

double click to drop anchor
single click
single click
double click

Selection examples

Select:

:G	Chain G
145:G	Residue 145 of Chain G
45-50:G	Residues 45 to 50 of Chain G
*.CA	all c-alphas
[Cys].CA	all Cys c-alphas
[Cys]:A.CA	all Cys c-alphas in Chain A

Use the following to execute Jmol commands:

Select:   aa:AsnGlnAspGluArgLysGlyAlaValIleLeuThrPheTyrTrpProMetSerThrCysHisCystine-----HydrophobicNeutralPolarChargedAcidicBasicAminoAromaticAliphaticHydrogenwhere:BondedLigandSurfaceBuried2ndry:HelixSheetTurn   BB:BackboneSidechainType:AllProteinNucleicSolventWaterHeteroIonsDNA:ATCGACGTUPyrimidinePurine
   Chain    Res No    Atom No

  Find within Å of the above selection
  

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Apply:    Wireframe       Color:cpkRedOrangeYellowGreenBlueCyanVioletBrownMagentaPinkLightGreenLightBlueLightYellowGrayBlackWhitePurple
Rocket          Cartoon    Transluc
Backbone    Ribbon
Spacefill    Dots    Halos    

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Show:    Show secondary struct H-bonds
Show all H-bonds

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Global:
   Stereo:
     None  Off  cross-eyed  wall-eyed
   Bkgrnd Color:cpkRedOrangeYellowGreenBlueCyanVioletBrownMagentaPinkLightGreenLightBlueLightYellowGrayBlackWhitePurple   HBonds
Rotate to current view

This is an example of a Jmol presentation (click on the "About" menu above for more info on Jmol).

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Some test stuff.

Color protein green using a link.

Test of a simple button. Make pretty.

yellowTest of a toggle button. Color protein yellow

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Presentation by Craig T. Martin, Department of Chemistry, University of Massachusetts. September 12, 2004.

Use the menu above to access its features.

About - provides information about this presentation, about Jmol and Jmol.js, and about JmolShell

Cmd - provides a larger command line for executing Jmol commands.

Help - provides help

Reset - Redraws the molecule to its starting view and rendering

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ABSTRACT:
Regulatory factor X (RFX) proteins are transcriptional activators that recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD). DNA-binding defects in the protein RFX5 cause bare lymphocyte syndrome or major histocompatibility antigen class II deficiency. RFX1, -2 and -3 regulate expression of other medically important gene products (for example, interleukin-5 receptor alpha chain, IL-5R alpha). Fusions of the ligand-binding domain of the oestrogen receptor with the DBD of RFX4 occur in some human breast tumours. Here we present a 1.5 A-resolution structure of two copies of the DBD of human RFX1 (hRFX1) binding cooperatively to a symmetrical X-box. hRFX1 is an unusual member of the winged-helix subfamily of helix-turn-helix proteins because it uses a beta-hairpin (or wing) to recognize DNA instead of the recognition helix typical of helix-turn-helix proteins. A new model for interactions between linker histones and DNA is proposed.