1JMN | Genus

Total Genus 8

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	8
sequence length	46
structure length	46
Chain Sequence	KSCCPNTTGRNIYNTCRFGGGSRQVCASLSGCKIISASTCPSDYPK

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__21583154559963402__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__21583154559963402__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1JMN/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__21583154559963402__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"21583154559963402","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1JMN/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__21583154559963402__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d29ac1ee0498bc1a29f3acb/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d29ac1ee0498bc1a29f3acb/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d29ac1ee0498bc1a29f3acb/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/5d29ac1ee0498bc1a29f3acb/pdb.gz): 203 ms

reading 46 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

46 atoms created

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

Time for creating model: 14 ms

Adding embedded #jmolscript: select ({0:45});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	Toxin
source organism	Viscum album
publication title	Solution Structure of the Viscotoxin A2 rcsb
molecule keywords	viscotoxin A2
total genus	8
structure length	46
sequence length	46
ec nomenclature
pdb deposition date	2001-07-19

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1350.10	Alpha Beta	2-Layer Sandwich	Crambin	Thionin-like	1jmnA00

1NBLA 1JXXA 1CRNA 1CCNA 2PLHA 1ED0A 1JXWA 1YV8A 2V9BA 2FD7A 1CBNA 2EYBA 2EYAA 1AB1A 1JMNA 1CXRA 1JXYA 3C8PA 1JXTA 3SZSA 4FC1A 2FD9A 1EJGA 3U7TA 1CNRA 1OKHA 2EYCA 1JMPA 2EYDA 3NIRA 1YVAA 3UE7B 1CCMA 1ORLA 1JXUA 1WUWA 1BHPA
chains in the Genus database with same CATH superfamily

1NBLA 1JXXA 1CRNA 1CCNA 2PLHA 1ED0A 1JXWA 1YV8A 2V9BA 1JNBA 2FD7A 1CBNA 2EYBA 2EYAA 1AB1A 1JMNA 1H5WA 1CXRA 1JXYA 3C8PA 1JXTA 3SZSA 4FC1A 2FD9A 1EJGA 3U7TA 1CNRA 1OKHA 2EYCA 1JMPA 2EYDA 3NIRA 1YVAA 3UE7B 1IJGA 1CCMA 1ORLA 1FOUA 1JXUA 1WUWA 1BHPA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1NBL A;  1JXX A;  1CRN A;  1CCN A;  2PLH A;  1ED0 A;  1JXW A;  1YV8 A;  2V9B A;  2FD7 A;  1CBN A;  2EYB A;  2EYA A;  1AB1 A;  1JMN A;  1CXR A;  1JXY A;  3C8P A;  1JXT A;  3SZS A;  4FC1 A;  2FD9 A;  1EJG A;  3U7T A;  1CNR A;  1OKH A;  2EYC A;  1JMP A;  2EYD A;  3NIR A;  1YVA A;  3UE7 B;  1CCM A;  1ORL A;  1JXU A;  1WUW A;  1BHP A; 
#chains in the Genus database with same CATH topology
 1NBL A;  1JXX A;  1CRN A;  1CCN A;  2PLH A;  1ED0 A;  1JXW A;  1YV8 A;  2V9B A;  1JNB A;  2FD7 A;  1CBN A;  2EYB A;  2EYA A;  1AB1 A;  1JMN A;  1H5W A;  1CXR A;  1JXY A;  3C8P A;  1JXT A;  3SZS A;  4FC1 A;  2FD9 A;  1EJG A;  3U7T A;  1CNR A;  1OKH A;  2EYC A;  1JMP A;  2EYD A;  3NIR A;  1YVA A;  3UE7 B;  1IJG A;  1CCM A;  1ORL A;  1FOU A;  1JXU A;  1WUW A;  1BHP A; 
#chains in the Genus database with same CATH homology
 1NBL A;  1JXX A;  1CRN A;  1CCN A;  2PLH A;  1ED0 A;  1JXW A;  1YV8 A;  2V9B A;  2FD7 A;  1CBN A;  2EYB A;  2EYA A;  1AB1 A;  1JMN A;  1CXR A;  1JXY A;  3C8P A;  1JXT A;  3SZS A;  4FC1 A;  2FD9 A;  1EJG A;  3U7T A;  1CNR A;  1OKH A;  2EYC A;  1JMP A;  2EYD A;  3NIR A;  1YVA A;  3UE7 B;  1CCM A;  1ORL A;  1JXU A;  1WUW A;  1BHP 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...

1JMNA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN