6AC3 | Genus

Total Genus 102

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	102
sequence length	432
structure length	419
Chain Sequence	IVNGDRPRDLVFPGTAGLQLYQSLYKYSYITDGIIDAHTNEVISYAQIFETSCRLAVSLEKYGLDHNNVVAICSENNIHFFGPLIAALYQGIPMATSNDMYTEREMIGHLNISKPCLMFCSKKSLPFILKVQKHLDFLKKVIVIDSMYDINGVECVFSFVSRYTDHAFDPVKFNPKEFDPLERTALIMTSSGTTGLPKGVVISHRSITIRFVHSSDPIYGTRIAPDTSILAIAPFHHAFGLFTALAYFPVGLKIVMVKKFEGEFFLKTIQNYKIASIVVPPPIMVYLAKSPLVDEYNLSSLTEIACGGSPLGRDIADKVAKRLKVHGILQGYGLTETCSALILSPMPYVQVKVIDINTGKALGPREKGEICFKSQMLMKGYHNNPQATRDALDKDGWLHTGDLGYYDEDRFIYVVDRLK

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__715695496820192__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__715695496820192__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/6ac3/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__715695496820192__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"715695496820192","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/6ac3/A/"

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__715695496820192__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d07181b354e787f38adf815/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d07181b354e787f38adf815/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d07181b354e787f38adf815/pdb.gz)

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

The Resolver thinks Pdb

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

Time for openFile(/file/5d07181b354e787f38adf815/pdb.gz): 2040 ms

reading 419 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

419 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 30 ms

Adding embedded #jmolscript: select ({0:418});backbone only;select *;

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

Chord Diagram

molecule tags	Luminescent protein
source organism	Phrixothrix hirtus
publication title	Beetle luciferases with naturally red- and blue-shifted emission. pubmed doi rcsb
molecule keywords	Red-bioluminescence eliciting luciferase
total genus	102
structure length	419
sequence length	432
chains with identical sequence	B, C, D
ec nomenclature
pdb deposition date	2018-07-24

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00501	AMP-binding	AMP-binding enzyme
A	PF13193	AMP-binding_C	AMP-binding enzyme C-terminal domain

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

...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...

6AC3A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations