2LW6 | Genus

Total Genus 9

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	9
sequence length	80
structure length	80
Chain Sequence	SFVQCNHHLLYNGRHWGTIRKKAGWAVRFYEEKPGQPKRLVAICKNASPVHCNYLKCTNLAAGFSAGTSTDVLSSGTVGS

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__010620239110668__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__010620239110668__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2LW6/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__010620239110668__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"010620239110668","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2LW6/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__010620239110668__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd508e90fea93bf241b6d8/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd508e90fea93bf241b6d8/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd508e90fea93bf241b6d8/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/5cfd508e90fea93bf241b6d8/pdb.gz): 1143 ms

reading 80 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

80 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:79});backbone only;select *;

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	Apoptosis
source organism	Magnaporthe oryzae
publication title	Solution structure of the Magnaporthe oryzae avirulence protein AvrPiz-t. pubmed doi rcsb
molecule keywords	AvrPiz-t protein
total genus	9
structure length	80
sequence length	80
ec nomenclature
pdb deposition date	2012-07-23

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

cath code	Class	Architecture	Topology	Homology	Domain
3.10.330.80	Alpha Beta	Roll	Vcp-like ATPase; Chain A, domain 2	Vcp-like ATPase; Chain A, domain 2	2lw6A00

2LW6A
chains in the Genus database with same CATH superfamily

5CD1A 3FPRA 3QC8A 3ZJTA 2MM2A 2YUJA 1CZ5A 4KO8A 4KODA 1QDNA 2GFAA 3BQBA 2PWYA 2QQSA 3ZJVA 1QCSA 2QQRA 5CCBA 3LHDA 1O54A 2YVLA 5FTLA 5EPPA 2LW6A 2Q1DX 5FTJA 3FPUA 2GF7A 3TIWA 4AQ7A 4KDLA 5C18A 3HU1A 5FTNA 5CCXA 5D6WA 2Q1AX 2Q19X 5D6XA 5EQJB 5DYGA 2Q18X 5B6CA 5GLFA 4ARCA 3QWZA 1ZC1A 3ZGZA 4FIBA 4AS1A 1WLFA 4RV0A 4KLNA 3QQ8A 5D6YA 2PJHB 5DYIA 1R7RA 2KY9A 3HU3A 3LGAA 5ERGB 4UC4A 3HU2A 3CF2A 1CR5A 4CQNA 3QQ7A 2XDPA 1S3SA 3MB5A 3ZJUA 2B25A 1I9GA 5FTKA 1CZ4A 5C1BA 5FTMA 2Q1CX 3FPTA 1E32A 2MM0A 4ARIA 2JV2A 4KDIA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2LW6 A; 
#chains in the Genus database with same CATH topology
 5CD1 A;  3FPR A;  3QC8 A;  3ZJT A;  2MM2 A;  2YUJ A;  1CZ5 A;  4KO8 A;  4KOD A;  1QDN A;  2GFA A;  3BQB A;  2PWY A;  2QQS A;  3ZJV A;  1QCS A;  2QQR A;  5CCB A;  3LHD A;  1O54 A;  2YVL A;  5FTL A;  5EPP A;  2LW6 A;  2Q1D X;  5FTJ A;  3FPU A;  2GF7 A;  3TIW A;  4AQ7 A;  4KDL A;  5C18 A;  3HU1 A;  5FTN A;  5CCX A;  5D6W A;  2Q1A X;  2Q19 X;  5D6X A;  5EQJ B;  5DYG A;  2Q18 X;  5B6C A;  5GLF A;  4ARC A;  3QWZ A;  1ZC1 A;  3ZGZ A;  4FIB A;  4AS1 A;  1WLF A;  4RV0 A;  4KLN A;  3QQ8 A;  5D6Y A;  2PJH B;  5DYI A;  1R7R A;  2KY9 A;  3HU3 A;  3LGA A;  5ERG B;  4UC4 A;  3HU2 A;  3CF2 A;  1CR5 A;  4CQN A;  3QQ7 A;  2XDP A;  1S3S A;  3MB5 A;  3ZJU A;  2B25 A;  1I9G A;  5FTK A;  1CZ4 A;  5C1B A;  5FTM A;  2Q1C X;  3FPT A;  1E32 A;  2MM0 A;  4ARI A;  2JV2 A;  4KDI A; 
#chains in the Genus database with same CATH homology
 5CD1 A;  3FPR A;  3QC8 A;  3ZJT A;  2MM2 A;  2YUJ A;  1CZ5 A;  4KO8 A;  4KOD A;  1QDN A;  2GFA A;  3BQB A;  2PWY A;  2QQS A;  3ZJV A;  1QCS A;  2QQR A;  5CCB A;  3LHD A;  1O54 A;  2YVL A;  5FTL A;  5EPP A;  2LW6 A;  2Q1D X;  5FTJ A;  3FPU A;  2GF7 A;  3TIW A;  4AQ7 A;  4KDL A;  5C18 A;  3HU1 A;  5FTN A;  5CCX A;  5D6W A;  2Q1A X;  2Q19 X;  5D6X A;  5EQJ B;  5DYG A;  2Q18 X;  5B6C A;  5GLF A;  4ARC A;  3QWZ A;  1ZC1 A;  3ZGZ A;  4FIB A;  4AS1 A;  1WLF A;  4RV0 A;  4KLN A;  3QQ8 A;  5D6Y A;  2PJH B;  5DYI A;  1R7R A;  2KY9 A;  3HU3 A;  3LGA A;  5ERG B;  4UC4 A;  3HU2 A;  3CF2 A;  1CR5 A;  4CQN A;  3QQ7 A;  2XDP A;  1S3S A;  3MB5 A;  3ZJU A;  2B25 A;  1I9G A;  5FTK A;  1CZ4 A;  5C1B A;  5FTM A;  2Q1C X;  3FPT A;  1E32 A;  2MM0 A;  4ARI A;  2JV2 A;  4KDI 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...

2LW6A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN