2KXS | Genus

Total Genus 12

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	12
sequence length	146
structure length	146
Chain Sequence	HSSGLEVLFQGPGSTVVATARGIFNSNGGVLSSIETGVSIIIPQGAIPEGVEQEIYFKVCRDNSILPPLDKEKGETLLSPLVMCGPHGLKFLKPVELRLPHCDPKTWQNKCLPGDPNYLVGANCVSVLIDHFGSGSGVVYGVVRRS

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__2746379285038576__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__2746379285038576__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2KXS/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__2746379285038576__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"2746379285038576","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2KXS/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__2746379285038576__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd4e0581a2fe2a04b241d1/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd4e0581a2fe2a04b241d1/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd4e0581a2fe2a04b241d1/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/5cfd4e0581a2fe2a04b241d1/pdb.gz): 416 ms

reading 146 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

146 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:145});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	Protein binding
source organism	Homo sapiens, synthetic, homo sapiens
publication title	Cdc42-dependent formation of the ZO-1/MRCKb complex at the leading edge controls cell migration pubmed doi rcsb
molecule keywords	Tight junction protein ZO-1, LINKER, peptide of Myocardium-e
total genus	12
structure length	146
sequence length	146
ec nomenclature
pdb deposition date	2010-05-12

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00791	ZU5	ZU5 domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.220.30	Mainly Beta	Sandwich	Chondroitinase Ac; Chain A, domain 3	Chondroitinase Ac; Chain A, domain 3	2kxsA00

2KXRA 3UD1A 2KXSA 3F59A 3KBTC 3KBUC 4D8OA 3UD2A
chains in the Genus database with same CATH superfamily

2Q1FA 4D6DA 2BRPA 1CB8A 1OJMA 4D6CA 1LOHA 1RWAA 3U7VA 4D6JA 1RWCA 2WMJA 1OJNA 1I8QA 1LXMA 2KXSA 4DLQA 1N7NA 3F59A 1HMWA 4D8OA 4D6GA 2X03A 2WMKA 1X1HA 2E22A 1F9GA 4D6IA 1HM2A 1N7RA 1RWHA 2WMFA 2WMIB 1LXKA 1OJOA 3UD1A 4DLOA 1HN0A 1RWGA 4D6EA 1OJPA 2WMIA 1N7PA 1W3YA 4D71A 2BRVX 4D6HA 1F1SA 1HMUA 1RWFA 2BRWA 1EGUA 1N7OA 1RW9A 2WMHA 1C82A 2WMGA 1N7QA 3KBUC 2E24A 3UD2A 4D72A 2WDAA 1J0NA 1J0MA 4D6FA 4D1IA 2KXRA 4D1JA 3PQIA 2WCOA 3QR8A 3KBTC 1X1IA 1HM3A 1X1JA
chains in the Genus database with same CATH topology

2KXRA 3UD1A 3PQIA 4DLOA 2KXSA 4DLQA 3F59A 3QR8A 3KBTC 3KBUC 4D8OA 3UD2A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2KXR A;  3UD1 A;  2KXS A;  3F59 A;  3KBT C;  3KBU C;  4D8O A;  3UD2 A; 
#chains in the Genus database with same CATH topology
 2Q1F A;  4D6D A;  2BRP A;  1CB8 A;  1OJM A;  4D6C A;  1LOH A;  1RWA A;  3U7V A;  4D6J A;  1RWC A;  2WMJ A;  1OJN A;  1I8Q A;  1LXM A;  2KXS A;  4DLQ A;  1N7N A;  3F59 A;  1HMW A;  4D8O A;  4D6G A;  2X03 A;  2WMK A;  1X1H A;  2E22 A;  1F9G A;  4D6I A;  1HM2 A;  1N7R A;  1RWH A;  2WMF A;  2WMI B;  1LXK A;  1OJO A;  3UD1 A;  4DLO A;  1HN0 A;  1RWG A;  4D6E A;  1OJP A;  2WMI A;  1N7P A;  1W3Y A;  4D71 A;  2BRV X;  4D6H A;  1F1S A;  1HMU A;  1RWF A;  2BRW A;  1EGU A;  1N7O A;  1RW9 A;  2WMH A;  1C82 A;  2WMG A;  1N7Q A;  3KBU C;  2E24 A;  3UD2 A;  4D72 A;  2WDA A;  1J0N A;  1J0M A;  4D6F A;  4D1I A;  2KXR A;  4D1J A;  3PQI A;  2WCO A;  3QR8 A;  3KBT C;  1X1I A;  1HM3 A;  1X1J A; 
#chains in the Genus database with same CATH homology
 2KXR A;  3UD1 A;  3PQI A;  4DLO A;  2KXS A;  4DLQ A;  3F59 A;  3QR8 A;  3KBT C;  3KBU C;  4D8O A;  3UD2 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...

2KXSA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations