4OZ6 | Genus

Total Genus 33

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	33
sequence length	202
structure length	171
Chain Sequence	AITGDALVALPEGESVRIADIVPGARPNSDNAIDLKVLDRHGNPVLADRLFHSGEHPVYTVRTVEGLRVTGTANHPLLCLVDVAGVPTLLWKLIDEIKPGDYAVIQRSAFVPGLVRFLAQAIADELTDGRFYYAKVASVTDAGVQPVYSLRVDACDAFITNGFVSHNTEAP

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__703029373381011__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__703029373381011__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4OZ6/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__703029373381011__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"703029373381011","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4OZ6/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__703029373381011__ ready

script 1 started

platformSpeed = 8

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	Isomerase
source organism	Mycobacterium xenopi
publication title	Structure of the branched intermediate in protein splicing. pubmed doi rcsb
molecule keywords	Mxe gyrA intein
total genus	33
structure length	171
sequence length	202
ec nomenclature	ec 5.99.1.3: Transferred entry: 5.6.2.3.
pdb deposition date	2014-02-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF14890	Intein_splicing	Intein splicing domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.170.16.10	Mainly Beta	Beta Complex	Endonuclease - Pi-scei; Chain A, domain 1	Hedgehog/Intein (Hint) domain	4oz6A00

2IMZA 1AM2A 1VDEA 4GIGA 4OZ6A 2IN9A 2LCJA 5K08A 2IN0A 1DQ3A 4KL5A 1EF0A 2CW8A 2CW7A 4O1RA 2JNQA 1MI8A 2LWYA 5I0AA 2LQMA 2IN8A 2L8LA 4O1SA 3NZMA 2JMZA 1ZD7A 3IGDA 4E2UA 1AT0A 1UM2A 2KEQA 1ZDEA 3IFJA 1GPPA 1JVAA 1LWTA 1DFAA 1LWSA 4KL6A 4E2TA
chains in the Genus database with same CATH superfamily

2IMZA 1AM2A 1VDEA 4GIGA 4OZ6A 2IN9A 2LCJA 5K08A 2IN0A 4LX3A 1DQ3A 4KL5A 1EF0A 2CW8A 2CW7A 4O1RA 2JNQA 1MI8A 2LWYA 5I0AA 2LQMA 2IN8A 2L8LA 4O1SA 3NZMA 2JMZA 1ZD7A 3IGDA 4E2UA 4QFQA 1AT0A 1UM2A 2KEQA 1ZDEA 3IFJA 1GPPA 1JVAA 1LWTA 1DFAA 1LWSA 4KL6A 4E2TA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2IMZ A;  1AM2 A;  1VDE A;  4GIG A;  4OZ6 A;  2IN9 A;  2LCJ A;  5K08 A;  2IN0 A;  1DQ3 A;  4KL5 A;  1EF0 A;  2CW8 A;  2CW7 A;  4O1R A;  2JNQ A;  1MI8 A;  2LWY A;  5I0A A;  2LQM A;  2IN8 A;  2L8L A;  4O1S A;  3NZM A;  2JMZ A;  1ZD7 A;  3IGD A;  4E2U A;  1AT0 A;  1UM2 A;  2KEQ A;  1ZDE A;  3IFJ A;  1GPP A;  1JVA A;  1LWT A;  1DFA A;  1LWS A;  4KL6 A;  4E2T A; 
#chains in the Genus database with same CATH topology
 2IMZ A;  1AM2 A;  1VDE A;  4GIG A;  4OZ6 A;  2IN9 A;  2LCJ A;  5K08 A;  2IN0 A;  4LX3 A;  1DQ3 A;  4KL5 A;  1EF0 A;  2CW8 A;  2CW7 A;  4O1R A;  2JNQ A;  1MI8 A;  2LWY A;  5I0A A;  2LQM A;  2IN8 A;  2L8L A;  4O1S A;  3NZM A;  2JMZ A;  1ZD7 A;  3IGD A;  4E2U A;  4QFQ A;  1AT0 A;  1UM2 A;  2KEQ A;  1ZDE A;  3IFJ A;  1GPP A;  1JVA A;  1LWT A;  1DFA A;  1LWS A;  4KL6 A;  4E2T A; 
#chains in the Genus database with same CATH homology
 2IMZ A;  1AM2 A;  1VDE A;  4GIG A;  4OZ6 A;  2IN9 A;  2LCJ A;  5K08 A;  2IN0 A;  1DQ3 A;  4KL5 A;  1EF0 A;  2CW8 A;  2CW7 A;  4O1R A;  2JNQ A;  1MI8 A;  2LWY A;  5I0A A;  2LQM A;  2IN8 A;  2L8L A;  4O1S A;  3NZM A;  2JMZ A;  1ZD7 A;  3IGD A;  4E2U A;  1AT0 A;  1UM2 A;  2KEQ A;  1ZDE A;  3IFJ A;  1GPP A;  1JVA A;  1LWT A;  1DFA A;  1LWS A;  4KL6 A;  4E2T 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...

4OZ6A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations