1QXA | Genus

Total Genus 64

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	64
sequence length	214
structure length	214
Chain Sequence	EDKQERANYEKLQQKFQMLMSKHQAHVRPQFESLEKINKDIVGWIKLSGTSLNYPVLQGKTNHDYLNLDFEREHRRKGSIFMDFRNELKNLNHNTILYGHHVGDNTMFDVLEDYLKQSFYEKHKIIEFDNKYGKYQLQVFSAYKTTTKDNYIRTDFENDQDYQQFLDETKRKSVINSDVNVTVKDRIMTLSTCEDAYSETTKRIVVVAKIIKVS

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__619638270175972__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__619638270175972__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1QXA/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__619638270175972__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"619638270175972","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1QXA/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__619638270175972__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfbe8518f36f252ee2d6e76/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfbe8518f36f252ee2d6e76/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfbe8518f36f252ee2d6e76/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/5cfbe8518f36f252ee2d6e76/pdb.gz): 1184 ms

reading 214 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

214 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:213});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	Hydrolase
source organism	Staphylococcus aureus
publication title	The structure of sortase B, a cysteine transpeptidase that tethers surface protein to the Staphylococcus aureus cell wall pubmed doi rcsb
molecule keywords	NPQTN specific sortase B
total genus	64
structure length	214
sequence length	214
ec nomenclature
pdb deposition date	2003-09-05

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF04203	Sortase	Sortase domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.40.260.10	Mainly Beta	Beta Barrel	Sortase; Chain: A;	Sortase	1qxaA00

1T2PA 3PSQA 4G1JA 4O8TA 5CUWA 4LFDA 3RCCA 2W1JA 2KIDA 1IJAA 1T2OA 2LN7A 3RE9A 5JCVA 4Y4QA 1QX6A 3O0PA 2RUIA 4G1HA 4D70A 3G66A 3RBKA 3FN6A 1QWZA 5K9AA 4UX7A 5GO5A 3RBJA 3TBEA 3RBIA 2KW8A 2WTSA 3TB7A 5B23A 1QXAA 1NG5A 4O8LA 2W1KA 2OQWA 3G69A 3FN7A 4O8LB 1T2WA 3FN5A 2OQZA 4D7WA 2XWGA 2MLMA 1RZ2A 5GYJA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1T2P A;  3PSQ A;  4G1J A;  4O8T A;  5CUW A;  4LFD A;  3RCC A;  2W1J A;  2KID A;  1IJA A;  1T2O A;  2LN7 A;  3RE9 A;  5JCV A;  4Y4Q A;  1QX6 A;  3O0P A;  2RUI A;  4G1H A;  4D70 A;  3G66 A;  3RBK A;  3FN6 A;  1QWZ A;  5K9A A;  4UX7 A;  5GO5 A;  3RBJ A;  3TBE A;  3RBI A;  2KW8 A;  2WTS A;  3TB7 A;  5B23 A;  1QXA A;  1NG5 A;  4O8L A;  2W1K A;  2OQW A;  3G69 A;  3FN7 A;  4O8L B;  1T2W A;  3FN5 A;  2OQZ A;  4D7W A;  2XWG A;  2MLM A;  1RZ2 A;  5GYJ A; 
#chains in the Genus database with same CATH topology
 1T2P A;  3PSQ A;  4G1J A;  4O8T A;  5CUW A;  4LFD A;  3RCC A;  2W1J A;  2KID A;  1IJA A;  1T2O A;  2LN7 A;  3RE9 A;  5JCV A;  4Y4Q A;  1QX6 A;  3O0P A;  2RUI A;  4G1H A;  4D70 A;  3G66 A;  3RBK A;  3FN6 A;  1QWZ A;  5K9A A;  4UX7 A;  5GO5 A;  3RBJ A;  3TBE A;  3RBI A;  2KW8 A;  2WTS A;  3TB7 A;  5B23 A;  1QXA A;  1NG5 A;  4O8L A;  2W1K A;  2OQW A;  3G69 A;  3FN7 A;  4O8L B;  1T2W A;  3FN5 A;  2OQZ A;  4D7W A;  2XWG A;  2MLM A;  1RZ2 A;  5GYJ A; 
#chains in the Genus database with same CATH homology
 1T2P A;  3PSQ A;  4G1J A;  4O8T A;  5CUW A;  4LFD A;  3RCC A;  2W1J A;  2KID A;  1IJA A;  1T2O A;  2LN7 A;  3RE9 A;  5JCV A;  4Y4Q A;  1QX6 A;  3O0P A;  2RUI A;  4G1H A;  4D70 A;  3G66 A;  3RBK A;  3FN6 A;  1QWZ A;  5K9A A;  4UX7 A;  5GO5 A;  3RBJ A;  3TBE A;  3RBI A;  2KW8 A;  2WTS A;  3TB7 A;  5B23 A;  1QXA A;  1NG5 A;  4O8L A;  2W1K A;  2OQW A;  3G69 A;  3FN7 A;  4O8L B;  1T2W A;  3FN5 A;  2OQZ A;  4D7W A;  2XWG A;  2MLM A;  1RZ2 A;  5GYJ 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...

1QXAA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations