2ZF3 | Genus

Total Genus 42

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	42
sequence length	188
structure length	186
Chain Sequence	REPPLLPARWSSAYVSYWSPMLPDDQLTSGYCWFDYERDICRIDGLFNPWSERDTGYRLWMSEVGNAASGRTWKQKVAYGRERTAEQLCERPLDDETGPFAELFLPRDVLRRLGARHIGRRVVLGREADGWRYQRPGKGPSTLYLDAASGTPLRMVTGDEASRASLRDFPNVSEAEIPDAVFAAKR

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__243629915629117__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__243629915629117__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2ZF3/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__243629915629117__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"243629915629117","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2ZF3/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__243629915629117__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfe1ea0b86e53f05baf2d80/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfe1ea0b86e53f05baf2d80/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfe1ea0b86e53f05baf2d80/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/5cfe1ea0b86e53f05baf2d80/pdb.gz): 425 ms

reading 186 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

186 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:185});backbone only;select *;

platformSpeed = 8

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

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

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

Jmol script terminated

loadScript /static/js/j2s/J/g3d/HermiteRenderer.js

loadScript /static/js/j2s/J/renderbio/BioMeshRenderer.js

loadScript /static/js/j2s/J/render/MeshRenderer.js

loadScript /static/js/j2s/J/shape/Mesh.js

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

publication title	Crystal structure of VioE, a key player in the construction of the molecular skeleton of violacein rcsb
molecule keywords	Hypothetical protein VioE
molecule tags	Antibiotic
source organism	Chromobacterium violaceum
total genus	42
structure length	186
sequence length	188
chains with identical sequence	B, C, D, E, F
ec nomenclature
pdb deposition date	2007-12-20

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF18234	VioE	Violacein biosynthetic enzyme VioE

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

cath code	Class	Architecture	Topology	Homology	Domain
2.50.20.30	Mainly Beta	Clam	outer membrane lipoprotein receptor (LolB), chain A	outer membrane lipoprotein receptor (LolB), chain A	2zf3A00

2ZF4A 3BMZA 2ZF3A
chains in the Genus database with same CATH superfamily

3M4WA 3BK5A 2YZYA 3BMZA 4EG9A 2ZPCA 2V43A 4EGDA 3BUUA 3WJTA 2P4BA 4KI3A 2ZF3A 3MH9A 2V42A 3KSNA 1IWLA 4QA8A 1IWNA 2ZF4A 3WJUA 2W7QA 2ZPDA 3MHAA 1UA8A 2BYOA 4MXTA 3MH8A 4Z48A 3WJVA 4ZRAA 1IWMA
chains in the Genus database with same CATH topology

3MHAA 3BMZA 4QA8A 4EG9A 2BYOA 2ZF4A 3MH8A 4EGDA 4ZRAA 3MH9A 2ZF3A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2ZF4 A;  3BMZ A;  2ZF3 A; 
#chains in the Genus database with same CATH topology
 3M4W A;  3BK5 A;  2YZY A;  3BMZ A;  4EG9 A;  2ZPC A;  2V43 A;  4EGD A;  3BUU A;  3WJT A;  2P4B A;  4KI3 A;  2ZF3 A;  3MH9 A;  2V42 A;  3KSN A;  1IWL A;  4QA8 A;  1IWN A;  2ZF4 A;  3WJU A;  2W7Q A;  2ZPD A;  3MHA A;  1UA8 A;  2BYO A;  4MXT A;  3MH8 A;  4Z48 A;  3WJV A;  4ZRA A;  1IWM A; 
#chains in the Genus database with same CATH homology
 3MHA A;  3BMZ A;  4QA8 A;  4EG9 A;  2BYO A;  2ZF4 A;  3MH8 A;  4EGD A;  4ZRA A;  3MH9 A;  2ZF3 A;

...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...

2ZF3A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations