3M4W | Genus

Total Genus 66

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	66
sequence length	291
structure length	284
Chain Sequence	PASGALLQQMNLASQSLNYELSFISINKQGVESLRYRHARLDNRPLAQLLQMDGPRREVVQRGNEISYFEPGLEPFTLNGDYIVDSLPSLIYTDFKRLSPYYDFISVGRTRIADRLCEVIRVVARDGTRYSYIVWMDTESKLPMRVDLLDRDGETLEQFRVIAFNVNQDISSSMQTLAKANLPPLLSVPVGEKAKFSWTPTWLPQGFSEVSSSRRMPIESRLYSDGLFSFSVNVNRATPSSTDQMLRTGRRTVSTSVRDNAEITIVGELPPQTAKRIAENIKFG

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__517683922202051__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__517683922202051__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3M4W/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__517683922202051__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"517683922202051","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3M4W/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__517683922202051__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cff863bac51c2a53d45abc5/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cff863bac51c2a53d45abc5/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cff863bac51c2a53d45abc5/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/5cff863bac51c2a53d45abc5/pdb.gz): 517 ms

reading 284 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

284 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:283});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	Structural basis for the negative regulation of bacterial stress response by RseB pubmed doi rcsb
molecule keywords	Sigma-E factor regulatory protein rseB
molecule tags	Signaling protein/signaling protein
source organism	Escherichia coli
total genus	66
structure length	284
sequence length	291
chains with identical sequence	B, C, D
ec nomenclature
pdb deposition date	2010-03-12

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF03888	MucB_RseB	MucB/RseB N-terminal domain
A	PF17188	MucB_RseB_C	MucB/RseB C-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.50.20.10	Mainly Beta	Clam	outer membrane lipoprotein receptor (LolB), chain A	Lipoprotein localisation LolA/LolB/LppX	3m4wA01

3WJTA 1IWNA 3BUUA 2V43A 3WJUA 4KI3A 2P4BA 3WJVA 2W7QA 2V42A 1UA8A 1IWMA 4Z48A 3BK5A 1IWLA 2ZPCA 2YZYA 3M4WA 3KSNA 4MXTA 2ZPDA
chains in the Genus database with same CATH superfamily

3WJTA 1IWNA 3BUUA 2V43A 3MH9A 4EG9A 3WJUA 4KI3A 2P4BA 3WJVA 2W7QA 2ZF3A 2V42A 4ZRAA 4MXTA 3MH8A 3MHAA 1UA8A 1IWMA 4Z48A 3BK5A 1IWLA 2ZPCA 2BYOA 2YZYA 3M4WA 4EGDA 3KSNA 4QA8A 3BMZA 2ZF4A 2ZPDA
chains in the Genus database with same CATH topology

3WJTA 1IWNA 3BUUA 2V43A 3WJUA 4KI3A 2P4BA 3WJVA 2W7QA 2V42A 1UA8A 1IWMA 4Z48A 3BK5A 1IWLA 2ZPCA 2YZYA 3M4WA 3KSNA 4MXTA 2ZPDA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3WJT A;  1IWN A;  3BUU A;  2V43 A;  3WJU A;  4KI3 A;  2P4B A;  3WJV A;  2W7Q A;  2V42 A;  1UA8 A;  1IWM A;  4Z48 A;  3BK5 A;  1IWL A;  2ZPC A;  2YZY A;  3M4W A;  3KSN A;  4MXT A;  2ZPD A; 
#chains in the Genus database with same CATH topology
 3WJT A;  1IWN A;  3BUU A;  2V43 A;  3MH9 A;  4EG9 A;  3WJU A;  4KI3 A;  2P4B A;  3WJV A;  2W7Q A;  2ZF3 A;  2V42 A;  4ZRA A;  4MXT A;  3MH8 A;  3MHA A;  1UA8 A;  1IWM A;  4Z48 A;  3BK5 A;  1IWL A;  2ZPC A;  2BYO A;  2YZY A;  3M4W A;  4EGD A;  3KSN A;  4QA8 A;  3BMZ A;  2ZF4 A;  2ZPD A; 
#chains in the Genus database with same CATH homology
 3WJT A;  1IWN A;  3BUU A;  2V43 A;  3WJU A;  4KI3 A;  2P4B A;  3WJV A;  2W7Q A;  2V42 A;  1UA8 A;  1IWM A;  4Z48 A;  3BK5 A;  1IWL A;  2ZPC A;  2YZY A;  3M4W A;  3KSN A;  4MXT A;  2ZPD 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...

3M4WA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations