1WIB | Genus

Total Genus 6

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	6
sequence length	92
structure length	92
Chain Sequence	GSSGSSGPPKFDPNEVKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQIEVVPSASALSGPSSG

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__889984715989397__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__889984715989397__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1WIB/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__889984715989397__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"889984715989397","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1WIB/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__889984715989397__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfc59f5151889812f84932c/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfc59f5151889812f84932c/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfc59f5151889812f84932c/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/5cfc59f5151889812f84932c/pdb.gz): 1478 ms

reading 92 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

92 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:91});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	Solution structure of the N-terminal domain from mouse hypothetical protein BAB22488 rcsb
molecule keywords	60S ribosomal protein L12
molecule tags	Ribosome
source organism	Mus musculus
total genus	6
structure length	92
sequence length	92
ec nomenclature
pdb deposition date	2004-05-28

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF03946	Ribosomal_L11_N	Ribosomal protein L11, N-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1550.10	Alpha Beta	2-Layer Sandwich	Ribosomal protein L11, N-terminal domain	Ribosomal protein L11/L12, N-terminal domain	1wibA00

2E35A 3J7ZI 3CJRB 3EGVB 2JQ7A 4V19K 2ZJQF 3CJSB 2K3FA 1MMSA 3J7YJ 3CJQB 4UY8I 5GAGJ 2E36A 5DM6F 2NXNB 1WIBA 3CF5F 2E34A 5GAHJ 5DM7F 5GADJ 2H8WA 2ZJPF 3CJTB
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2E35 A;  3J7Z I;  3CJR B;  3EGV B;  2JQ7 A;  4V19 K;  2ZJQ F;  3CJS B;  2K3F A;  1MMS A;  3J7Y J;  3CJQ B;  4UY8 I;  5GAG J;  2E36 A;  5DM6 F;  2NXN B;  1WIB A;  3CF5 F;  2E34 A;  5GAH J;  5DM7 F;  5GAD J;  2H8W A;  2ZJP F;  3CJT B; 
#chains in the Genus database with same CATH topology
 2E35 A;  3J7Z I;  3CJR B;  3EGV B;  2JQ7 A;  4V19 K;  2ZJQ F;  3CJS B;  2K3F A;  1MMS A;  3J7Y J;  3CJQ B;  4UY8 I;  5GAG J;  2E36 A;  5DM6 F;  2NXN B;  1WIB A;  3CF5 F;  2E34 A;  5GAH J;  5DM7 F;  5GAD J;  2H8W A;  2ZJP F;  3CJT B; 
#chains in the Genus database with same CATH homology
 2E35 A;  3J7Z I;  3CJR B;  3EGV B;  2JQ7 A;  4V19 K;  2ZJQ F;  3CJS B;  2K3F A;  1MMS A;  3J7Y J;  3CJQ B;  4UY8 I;  5GAG J;  2E36 A;  5DM6 F;  2NXN B;  1WIB A;  3CF5 F;  2E34 A;  5GAH J;  5DM7 F;  5GAD J;  2H8W A;  2ZJP F;  3CJT 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...

1WIBA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations