4KG9 | Genus

Total Genus 23

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	23
sequence length	143
structure length	138
Chain Sequence	TSWRSEATFQFTVERFSRLSESVLSPPCFVRNLPWKIMVMPRFYQKSVGFFLQCNAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHGVAW

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__2731890223280584__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__2731890223280584__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4KG9/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__2731890223280584__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"2731890223280584","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4KG9/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__2731890223280584__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0063d78718a54cfcad3bd4/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0063d78718a54cfcad3bd4/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0063d78718a54cfcad3bd4/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/5d0063d78718a54cfcad3bd4/pdb.gz): 319 ms

reading 138 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

138 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:137});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	Hydrolase
source organism	Homo sapiens
publication title	A role for USP7 in DNA replication. pubmed doi rcsb
molecule keywords	Ubiquitin carboxyl-terminal hydrolase 7
total genus	23
structure length	138
sequence length	143
ec nomenclature	ec 3.4.19.12: Ubiquitinyl hydrolase 1.
pdb deposition date	2013-04-29

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00917	MATH	MATH domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.210.10	Mainly Beta	Sandwich	Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A	Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A	4kg9A00

4M4EA 2F1ZA 4GWNA 4GWMA 2FOOA 5H9MA 1FLKA 4Z8MA 3HSVA 2FOJA 1D00A 2GKWA 1RF3A 1D0JA 3HQMA 4KG9A 3HU6A 2AN6A 1CA4A 3MQSC 3IVBA 4I7DA 3IVVA 1QSCA 3IVQA 1CZYA 1LB4A 2FOPA 5E1TA 3HQHA 4K8UA 3ZJBA 4C9ZA 3MQRA 1FLLA 4CA1A 1K2FA 2A25A 1LB5A 2F1XA 4O1VA 4GJHA 4YSIA 4GHUA 1LB6A 1L0AA 1F3VB 1KZZA 1D0AA 1CZZA 1ZMSA 2F1WA 2F1YA 4I7CA 1D01A 1YZEA 4I7BA 1CA9A 3HQLA 4JJQA 4X3GA 2CR2A 2XXNA 1YY6A 3HQIA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 4M4E A;  2F1Z A;  4GWN A;  4GWM A;  2FOO A;  5H9M A;  1FLK A;  4Z8M A;  3HSV A;  2FOJ A;  1D00 A;  2GKW A;  1RF3 A;  1D0J A;  3HQM A;  4KG9 A;  3HU6 A;  2AN6 A;  1CA4 A;  3MQS C;  3IVB A;  4I7D A;  3IVV A;  1QSC A;  3IVQ A;  1CZY A;  1LB4 A;  2FOP A;  5E1T A;  3HQH A;  4K8U A;  3ZJB A;  4C9Z A;  3MQR A;  1FLL A;  4CA1 A;  1K2F A;  2A25 A;  1LB5 A;  2F1X A;  4O1V A;  4GJH A;  4YSI A;  4GHU A;  1LB6 A;  1L0A A;  1F3V B;  1KZZ A;  1D0A A;  1CZZ A;  1ZMS A;  2F1W A;  2F1Y A;  4I7C A;  1D01 A;  1YZE A;  4I7B A;  1CA9 A;  3HQL A;  4JJQ A;  4X3G A;  2CR2 A;  2XXN A;  1YY6 A;  3HQI A; 
#chains in the Genus database with same CATH topology
 4M4E A;  2F1Z A;  4GWN A;  4GWM A;  2FOO A;  5H9M A;  1FLK A;  4Z8M A;  3HSV A;  2FOJ A;  1D00 A;  2GKW A;  1RF3 A;  1D0J A;  3HQM A;  4KG9 A;  3HU6 A;  2AN6 A;  1CA4 A;  3MQS C;  3IVB A;  4I7D A;  3IVV A;  1QSC A;  3IVQ A;  1CZY A;  1LB4 A;  2FOP A;  5E1T A;  3HQH A;  4K8U A;  3ZJB A;  4C9Z A;  3MQR A;  1FLL A;  4CA1 A;  1K2F A;  2A25 A;  1LB5 A;  2F1X A;  4O1V A;  4GJH A;  4YSI A;  4GHU A;  1LB6 A;  1L0A A;  1F3V B;  1KZZ A;  1D0A A;  1CZZ A;  1ZMS A;  2F1W A;  2F1Y A;  4I7C A;  1D01 A;  1YZE A;  4I7B A;  1CA9 A;  3HQL A;  4JJQ A;  4X3G A;  2CR2 A;  2XXN A;  1YY6 A;  3HQI A; 
#chains in the Genus database with same CATH homology
 4M4E A;  2F1Z A;  4GWN A;  4GWM A;  2FOO A;  5H9M A;  1FLK A;  4Z8M A;  3HSV A;  2FOJ A;  1D00 A;  2GKW A;  1RF3 A;  1D0J A;  3HQM A;  4KG9 A;  3HU6 A;  2AN6 A;  1CA4 A;  3MQS C;  3IVB A;  4I7D A;  3IVV A;  1QSC A;  3IVQ A;  1CZY A;  1LB4 A;  2FOP A;  5E1T A;  3HQH A;  4K8U A;  3ZJB A;  4C9Z A;  3MQR A;  1FLL A;  4CA1 A;  1K2F A;  2A25 A;  1LB5 A;  2F1X A;  4O1V A;  4GJH A;  4YSI A;  4GHU A;  1LB6 A;  1L0A A;  1F3V B;  1KZZ A;  1D0A A;  1CZZ A;  1ZMS A;  2F1W A;  2F1Y A;  4I7C A;  1D01 A;  1YZE A;  4I7B A;  1CA9 A;  3HQL A;  4JJQ A;  4X3G A;  2CR2 A;  2XXN A;  1YY6 A;  3HQI 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...

4KG9A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations