5C5S | Genus

Total Genus 73

Loading diagram...

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	73
sequence length	210
structure length	210
Chain Sequence	FPGVEPGHFGVCVDSLTSDKASVPIVLEKLLEHVEMHGLYTEGLYRKSGAANRTRELRQALQTDPAAVKLENFPIHAITGVLKQWLRELPEPLMTFAQYGDFLRAVELPEKQEQLAAIYAVLEHLPEANHNSLERLIFHLVKVALLEDVNRMSPGALAIIFAPCLLRCPDNSDPLTSMKDVLKITTCVEMLIKEQMRKYKVKMEEISQLE

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__306422314229204__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__306422314229204__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/5C5S/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__306422314229204__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"306422314229204","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/5C5S/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__306422314229204__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d042bb93012902a828b85b0/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d042bb93012902a828b85b0/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d042bb93012902a828b85b0/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/5d042bb93012902a828b85b0/pdb.gz): 609 ms

reading 210 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

210 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:209});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	Myo9b is a key player in SLIT/ROBO-mediated lung tumor suppression pubmed doi rcsb
molecule keywords	Unconventional myosin-IXb
molecule tags	Signaling protein
source organism	Homo sapiens
total genus	73
structure length	210
sequence length	210
chains with identical sequence	B, C, D
ec nomenclature
pdb deposition date	2015-06-22

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00620	RhoGAP	RhoGAP domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.555.10	Mainly Alpha	Orthogonal Bundle	Phosphatidylinositol 3-kinase; Chain A	Rho GTPase activation protein	5c5sA00

2OVJA 1XA6A 1AM4A 3WPQA 2XS6A 1TX4A 3EAPA 3IUGA 2EE4A 2QV2A 3BYIA 3MSXB 1F7CA 3WPSA 2OSAA 2EE5A 3KUQA 3CXLA 5HPYA 1GRNB 1OW3A 2MBGA 5C2JA 5JCPA 3QISA 5IRCA 1PBWA 5JD0A 3FK2A 5C5SA 1RGPA 2NGRB 3W6RA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2OVJ A;  1XA6 A;  1AM4 A;  3WPQ A;  2XS6 A;  1TX4 A;  3EAP A;  3IUG A;  2EE4 A;  2QV2 A;  3BYI A;  3MSX B;  1F7C A;  3WPS A;  2OSA A;  2EE5 A;  3KUQ A;  3CXL A;  5HPY A;  1GRN B;  1OW3 A;  2MBG A;  5C2J A;  5JCP A;  3QIS A;  5IRC A;  1PBW A;  5JD0 A;  3FK2 A;  5C5S A;  1RGP A;  2NGR B;  3W6R A; 
#chains in the Genus database with same CATH topology
 2OVJ A;  1XA6 A;  1AM4 A;  3WPQ A;  2XS6 A;  1TX4 A;  3EAP A;  3IUG A;  2EE4 A;  2QV2 A;  3BYI A;  3MSX B;  1F7C A;  3WPS A;  2OSA A;  2EE5 A;  3KUQ A;  3CXL A;  5HPY A;  1GRN B;  1OW3 A;  2MBG A;  5C2J A;  5JCP A;  3QIS A;  5IRC A;  1PBW A;  5JD0 A;  3FK2 A;  5C5S A;  1RGP A;  2NGR B;  3W6R A; 
#chains in the Genus database with same CATH homology
 2OVJ A;  1XA6 A;  1AM4 A;  3WPQ A;  2XS6 A;  1TX4 A;  3EAP A;  3IUG A;  2EE4 A;  2QV2 A;  3BYI A;  3MSX B;  1F7C A;  3WPS A;  2OSA A;  2EE5 A;  3KUQ A;  3CXL A;  5HPY A;  1GRN B;  1OW3 A;  2MBG A;  5C2J A;  5JCP A;  3QIS A;  5IRC A;  1PBW A;  5JD0 A;  3FK2 A;  5C5S A;  1RGP A;  2NGR B;  3W6R 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...

5C5SA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations