1LZW | Genus

Total Genus 24

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	24
sequence length	91
structure length	91
Chain Sequence	EKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVAYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA

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__550499545498866__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__550499545498866__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1LZW/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__550499545498866__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"550499545498866","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1LZW/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__550499545498866__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfb8deb432703609ccbc4e1/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfb8deb432703609ccbc4e1/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfb8deb432703609ccbc4e1/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/5cfb8deb432703609ccbc4e1/pdb.gz): 71 ms

reading 91 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

91 atoms created

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

Time for creating model: 15 ms

Adding embedded #jmolscript: select ({0:90});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	Chaperone
source organism	Escherichia coli
publication title	Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA pubmed doi rcsb
molecule keywords	Protein yljA
total genus	24
structure length	91
sequence length	91
ec nomenclature
pdb deposition date	2002-06-11

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02617	ClpS	ATP-dependent Clp protease adaptor protein ClpS

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1390.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein L30; Chain: A,	Ribosomal Protein L30; Chain: A,	1lzwA00

2WA8A 1MBUC 1MG9A 2W9RA 3G1BA 3O2OA 3GQ1A 4YJMA 3DNJA 3O1FA 1LZWA 1R6QC 3O1FB 3G3PA 1CTFA 1RQUA 4YKAA 1R6OC 3O2BA 1RQVA 1RQSA 4YJXA 1MBVB 2WA9A 1DD4A 3G19A 3GW1A 3GQ0A 3O2HA 1DD3A 1MBXC
chains in the Genus database with same CATH superfamily

1MWUA 4WFAW 5HL7W 2W9RA 3G1BA 4U67W 3GQ1A 1QVGV 1QVFV 3W7SA 3DNJA 4BL2A 4DKIA 3CCEW 5DM7W 3CCSW 1RQUA 1K9MX 4UY8Z 3CCUW 1K73X 2ZJQW 1Q86X 3CC7W 3CXCV 4IOCW 1MWSA 3G19A 4WF9W 1VQ5W 1VQMW 3J7ZZ 3CD6W 3D3IA 3CPWV 1MBXC 1VQ8W 3O2OA 1VQQA 3ZG0A 5GADa 1S72W 1LZWA 3O1FB 2ZJPW 1VQ4W 1YITW 3CCLW 1VQOW 1CTFA 5M19A 3W7WA 3G71W 1VQKW 1YIJW 1W2BV 1VQ7W 5GAHa 4YKAA 1NJIX 1VQ9W 1MWTA 5DM6W 2OTLW 1MBVB 3CMAW 3CF5W 4WFBW 3CC2W 3CC4W 1JJ2V 4CPKA 3CCQW 5M1AA 1VQNW 3GQ0A 2QA4W 1MBUC 1YI2W 1VQLW 5GW7A 3OW2V 5CA3A 3O1FA 1R6QC 1KQSV 4BL3A 3G3PA 3ZFZA 1M90X 1R6OC 3CCRW 1Q82X 3PIOW 3O2BA 3PIPW 3I55W 1RQSA 4YJXA 3W7TA 2WA9A 1YJ9W 1Q81X 2OTJW 1N8RX 1DD4A 3GW1A 1YHQW 1Q7YX 1YJWW 5GAEa 4CJNA 1MWRA 3O2HA 1BXYA 1KC8X 1KD1X 2WA8A 1MG9A 1VQ6W 3I56W 3CCVW 4IOAW 1VQPW 5M18A 1K8AX 4IO9W 5JVHW 5GAGa 3G6EW 1YJNW 3W7XA 4WCEW 1RQVA 5JVGW 3ZG5A 3G4SW 4WFNW 2QEXW 3CCJW 3W7UA 1M1KX 3CMEW 3CCMW 1DD3A 3DLLW 2ZJRW 4YJMA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2WA8 A;  1MBU C;  1MG9 A;  2W9R A;  3G1B A;  3O2O A;  3GQ1 A;  4YJM A;  3DNJ A;  3O1F A;  1LZW A;  1R6Q C;  3O1F B;  3G3P A;  1CTF A;  1RQU A;  4YKA A;  1R6O C;  3O2B A;  1RQV A;  1RQS A;  4YJX A;  1MBV B;  2WA9 A;  1DD4 A;  3G19 A;  3GW1 A;  3GQ0 A;  3O2H A;  1DD3 A;  1MBX C; 
#chains in the Genus database with same CATH topology
 1MWU A;  4WFA W;  5HL7 W;  2W9R A;  3G1B A;  4U67 W;  3GQ1 A;  1QVG V;  1QVF V;  3W7S A;  3DNJ A;  4BL2 A;  4DKI A;  3CCE W;  5DM7 W;  3CCS W;  1RQU A;  1K9M X;  4UY8 Z;  3CCU W;  1K73 X;  2ZJQ W;  1Q86 X;  3CC7 W;  3CXC V;  4IOC W;  1MWS A;  3G19 A;  4WF9 W;  1VQ5 W;  1VQM W;  3J7Z Z;  3CD6 W;  3D3I A;  3CPW V;  1MBX C;  1VQ8 W;  3O2O A;  1VQQ A;  3ZG0 A;  5GAD a;  1S72 W;  1LZW A;  3O1F B;  2ZJP W;  1VQ4 W;  1YIT W;  3CCL W;  1VQO W;  1CTF A;  5M19 A;  3W7W A;  3G71 W;  1VQK W;  1YIJ W;  1W2B V;  1VQ7 W;  5GAH a;  4YKA A;  1NJI X;  1VQ9 W;  1MWT A;  5DM6 W;  2OTL W;  1MBV B;  3CMA W;  3CF5 W;  4WFB W;  3CC2 W;  3CC4 W;  1JJ2 V;  4CPK A;  3CCQ W;  5M1A A;  1VQN W;  3GQ0 A;  2QA4 W;  1MBU C;  1YI2 W;  1VQL W;  5GW7 A;  3OW2 V;  5CA3 A;  3O1F A;  1R6Q C;  1KQS V;  4BL3 A;  3G3P A;  3ZFZ A;  1M90 X;  1R6O C;  3CCR W;  1Q82 X;  3PIO W;  3O2B A;  3PIP W;  3I55 W;  1RQS A;  4YJX A;  3W7T A;  2WA9 A;  1YJ9 W;  1Q81 X;  2OTJ W;  1N8R X;  1DD4 A;  3GW1 A;  1YHQ W;  1Q7Y X;  1YJW W;  5GAE a;  4CJN A;  1MWR A;  3O2H A;  1BXY A;  1KC8 X;  1KD1 X;  2WA8 A;  1MG9 A;  1VQ6 W;  3I56 W;  3CCV W;  4IOA W;  1VQP W;  5M18 A;  1K8A X;  4IO9 W;  5JVH W;  5GAG a;  3G6E W;  1YJN W;  3W7X A;  4WCE W;  1RQV A;  5JVG W;  3ZG5 A;  3G4S W;  4WFN W;  2QEX W;  3CCJ W;  3W7U A;  1M1K X;  3CME W;  3CCM W;  1DD3 A;  3DLL W;  2ZJR W;  4YJM A; 
#chains in the Genus database with same CATH homology
 2WA8 A;  1MBU C;  1MG9 A;  2W9R A;  3G1B A;  3O2O A;  3GQ1 A;  4YJM A;  3DNJ A;  3O1F A;  1LZW A;  1R6Q C;  3O1F B;  3G3P A;  1CTF A;  1RQU A;  4YKA A;  1R6O C;  3O2B A;  1RQV A;  1RQS A;  4YJX A;  1MBV B;  2WA9 A;  1DD4 A;  3G19 A;  3GW1 A;  3GQ0 A;  3O2H A;  1DD3 A;  1MBX C;

...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...

1LZWA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations