1YTF | Genus

Total Genus 7

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	7
sequence length	46
structure length	46
Chain Sequence	ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEWV

Loading diagram...

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

loadScript /static/js/j2s/core/package.js

loadScript /static/js/j2s/core/corejmol.z.js

loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__996608710464854__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__996608710464854__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1YTF/C/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__996608710464854__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"996608710464854","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1YTF/C/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__996608710464854__ ready

script 1 started

platformSpeed = 8

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

publication title	Crystal structure of a yeast TFIIA/TBP/DNA complex. pubmed doi rcsb
molecule keywords	DNA (5'-D(TPGPTPAPTPGPTPAPTPAPTPAPAPAPAPC)-3
molecule tags	Transcription/dna
source organism	Saccharomyces cerevisiae
total genus	7
structure length	46
sequence length	46
ec nomenclature
pdb deposition date	1996-04-05

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
2.30.18.10	Mainly Beta	Roll	TATA box binding Protein, subunit D; domain 2	Transcription factor IIA (TFIIA), beta-barrel domain	1ytfC00

1RM1B 5IYDO 1NVPD 1NH2D 1NH2C 1RM1C 1NVPC 1YTFD 5IYCO 5IYBO 1YTFC
chains in the Genus database with same CATH superfamily

1RM1B 5IYDO 1NVPD 1NH2D 1NH2C 1RM1C 1NVPC 1YTFD 5IYCO 5IYBO 1YTFC
chains in the Genus database with same CATH topology

1RM1B 5IYDO 1NVPD 1NH2D 1NH2C 1RM1C 1NVPC 1YTFD 5IYCO 5IYBO 1YTFC
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 1RM1 B;  5IYD O;  1NVP D;  1NH2 D;  1NH2 C;  1RM1 C;  1NVP C;  1YTF D;  5IYC O;  5IYB O;  1YTF C; 
#chains in the Genus database with same CATH topology
 1RM1 B;  5IYD O;  1NVP D;  1NH2 D;  1NH2 C;  1RM1 C;  1NVP C;  1YTF D;  5IYC O;  5IYB O;  1YTF C; 
#chains in the Genus database with same CATH homology
 1RM1 B;  5IYD O;  1NVP D;  1NH2 D;  1NH2 C;  1RM1 C;  1NVP C;  1YTF D;  5IYC O;  5IYB O;  1YTF C;

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

1YTFC

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization