2JV8 | Genus

Total Genus 13

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	13
sequence length	73
structure length	73
Chain Sequence	MTHHTEVFEGGTIDIEDDTSLTINGKEISYVHDAVKNKWSSRYLPYTQYDSLLDLARAIIRDTVEFSGVKEGS

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__086590471836506__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__086590471836506__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2JV8/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__086590471836506__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"086590471836506","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2JV8/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__086590471836506__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd49ac885c5ce14bced748/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd49ac885c5ce14bced748/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd49ac885c5ce14bced748/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/5cfd49ac885c5ce14bced748/pdb.gz): 168 ms

reading 73 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

73 atoms created

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

Time for creating model: 16 ms

Adding embedded #jmolscript: select ({0:72});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

molecule tags	Structural genomics, unknown function
source organism	Nitrosomonas europaea atcc 19718
publication title	Solution NMR structure of protein NE1242 from Nitrosomonas europaea. rcsb
molecule keywords	Uncharacterized protein NE1242
total genus	13
structure length	73
sequence length	73
ec nomenclature
pdb deposition date	2007-09-12

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1880.10	Alpha Beta	2-Layer Sandwich	protein ne1242 fold	protein ne1242 domain like	2jv8A00

3AWSB 1WX4B 2AHKB 2ZMYB 2ZWEB 3AX0B 3AWZB 2AHLB 1WXCB 3AWTB 1WX2B 3AWXB 3AWYB 2JV8A 2ZMXB 2ZWDB 1WX5B 2ZMZB 2ZWFB 3AWVB 3AWWB 3AWUB 2ZWGB
chains in the Genus database with same CATH superfamily

1Z02A 4NBGA 4NBDA 3AWSB 4NBBA 3VMHA 4NBCA 1WX4B 3VMGA 4NB8A 4NB9A 2AHKB 1Z01A 2ZMYB 4NBEA 3VMIA 2ZWEB 4NBHA 3GKQA 3GCFA 3AX0B 3AWZB 4NBAA 2AHLB 1WW9A 1WXCB 3AWTB 1WX2B 2DE5A 3AWXB 1Z03A 3AWYB 2JV8A 2ZMXB 2ZWDB 1WX5B 2ZMZB 2ZWFB 2DE7A 3AWVB 2DE6A 3AWWB 3AWUB 4NBFA 2ZWGB
chains in the Genus database with same CATH topology

3AWSB 1WX4B 2AHKB 2ZMYB 2ZWEB 3AX0B 3AWZB 2AHLB 1WXCB 3AWTB 1WX2B 3AWXB 3AWYB 2JV8A 2ZMXB 2ZWDB 1WX5B 2ZMZB 2ZWFB 3AWVB 3AWWB 3AWUB 2ZWGB
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3AWS B;  1WX4 B;  2AHK B;  2ZMY B;  2ZWE B;  3AX0 B;  3AWZ B;  2AHL B;  1WXC B;  3AWT B;  1WX2 B;  3AWX B;  3AWY B;  2JV8 A;  2ZMX B;  2ZWD B;  1WX5 B;  2ZMZ B;  2ZWF B;  3AWV B;  3AWW B;  3AWU B;  2ZWG B; 
#chains in the Genus database with same CATH topology
 1Z02 A;  4NBG A;  4NBD A;  3AWS B;  4NBB A;  3VMH A;  4NBC A;  1WX4 B;  3VMG A;  4NB8 A;  4NB9 A;  2AHK B;  1Z01 A;  2ZMY B;  4NBE A;  3VMI A;  2ZWE B;  4NBH A;  3GKQ A;  3GCF A;  3AX0 B;  3AWZ B;  4NBA A;  2AHL B;  1WW9 A;  1WXC B;  3AWT B;  1WX2 B;  2DE5 A;  3AWX B;  1Z03 A;  3AWY B;  2JV8 A;  2ZMX B;  2ZWD B;  1WX5 B;  2ZMZ B;  2ZWF B;  2DE7 A;  3AWV B;  2DE6 A;  3AWW B;  3AWU B;  4NBF A;  2ZWG B; 
#chains in the Genus database with same CATH homology
 3AWS B;  1WX4 B;  2AHK B;  2ZMY B;  2ZWE B;  3AX0 B;  3AWZ B;  2AHL B;  1WXC B;  3AWT B;  1WX2 B;  3AWX B;  3AWY B;  2JV8 A;  2ZMX B;  2ZWD B;  1WX5 B;  2ZMZ B;  2ZWF B;  3AWV B;  3AWW B;  3AWU B;  2ZWG B;

...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...

2JV8A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN