2I3Q | Genus

Total Genus 45

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	45
sequence length	152
structure length	152
Chain Sequence	NTKYNKEFLLYLAGFVDGDGSIIAQIAPNQSYKFKHQLSLTFVVTQKTQRRWFLDKLVDEIGVGYVRDRGSVSDYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD

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__431181885555174__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__431181885555174__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2I3Q/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__431181885555174__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"431181885555174","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2I3Q/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__431181885555174__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d252a453ae3aa23095315cd/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d252a453ae3aa23095315cd/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d252a453ae3aa23095315cd/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/5d252a453ae3aa23095315cd/pdb.gz): 522 ms

reading 152 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

152 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:151});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	Hydrolase/dna
source organism	Chlamydomonas reinhardtii
publication title	Homing endonuclease I-CreI derivatives with novel DNA target specificities. pubmed doi rcsb
molecule keywords	5'-D(GPCPAPAPAPAPCPGPAPCPGPTPGPAPGPTPCPAP*
total genus	45
structure length	152
sequence length	152
chains with identical sequence	B
ec nomenclature	ec 3.1.-.-:
pdb deposition date	2006-08-20

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00961	LAGLIDADG_1	LAGLIDADG endonuclease

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

cath code	Class	Architecture	Topology	Homology	Domain
3.10.28.10	Alpha Beta	Roll	Endonuclease I-creI	Homing endonucleases	2i3qA00

1LWSA 2VS8A 1U0DA 5A74A 4AQXA 3MXBA 2VBLA 5E67A 4UN9G 4UN7G 1BP7A 3C0WA 1T9IA 5A0MB 2VBNB 1B24A 4UN9A 4Z1ZA 4UN7A 5E5OA 3FD2A 3KO2A 5AK9A 1G9YA 4LOXA 2VS7A 2I3QA 3QQYA 4UNCA 1VDEA 3HYIA 3MXBB 2XE0B 1AF5A 2VBLB 4UNAA 1M5XA 2VBOB 2XE0A 3E54A 5AKNA 3MIPA 4UT0A 3HYJA 1T9JA 2VBJA 4D6OA 2VBOA 1G9ZA 1DQ3A 4UN8G 1R7MA 3C0XA 1DFAA 5A0WA 4UN8A 4YITA 4LQ0A 4EFJA 1UM2A 2VBJB 4Z1XA 4AQUA 3MX9A 2AB5A 1JVAA 4UNBA 4Z20A 2DCHX 3MISA 4AAGA 2FLDA 1N3EA 3OOLA 5AKMA 2QOJZ 1MOWA 1LWTA 2I3PA 1U0CA 2O7MA 1EF0A 5A77A 2CW7A 2EX5A 4AABA 5A78A 3R7PA 3MXAA 3EH8A 4AAEA 5E5SA 4YHXA 5E63A 4AAFA 5A0MA 2VBNA 1P8KZ 3OORA 1N3FA 5AKFA 5A72A 4YISA 4AADA 2CW8A 3UVFA 4D6NA
chains in the Genus database with same CATH superfamily

1LWSA 2VS8A 1U0DA 5A74A 4AQXA 3MXBA 4KZSA 2VBLA 5E67A 4UN9G 4UN7G 1BP7A 3C0WA 1T9IA 5A0MB 2VBNB 1B24A 4UN9A 4Z1ZA 4UN7A 5E5OA 3FD2A 3KO2A 5AK9A 1G9YA 4LOXA 2VS7A 2I3QA 3QQYA 4UNCA 1VDEA 3HYIA 3MXBB 2XE0B 1AF5A 2VBLB 4UNAA 1M5XA 2VBOB 2XE0A 3E54A 5AKNA 3MIPA 4UT0A 3HYJA 1T9JA 2VBJA 4D6OA 2VBOA 1G9ZA 1DQ3A 4UN8G 1R7MA 3C0XA 1DFAA 5A0WA 4UN8A 4YITA 4LQ0A 4EFJA 1UM2A 2VBJB 4Z1XA 4AQUA 3MX9A 2AB5A 1JVAA 4UNBA 4Z20A 2DCHX 3MISA 4AAGA 2FLDA 1N3EA 3OOLA 5AKMA 2QOJZ 1MOWA 1LWTA 2I3PA 1U0CA 2O7MA 1EF0A 5A77A 2CW7A 2EX5A 4AABA 5A78A 3R7PA 3MXAA 3EH8A 4AAEA 5E5SA 4YHXA 5E63A 4AAFA 5A0MA 2VBNA 1P8KZ 3OORA 2F4LA 1N3FA 5AKFA 5A72A 4YISA 4AADA 2CW8A 3UVFA 4D6NA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1LWS A;  2VS8 A;  1U0D A;  5A74 A;  4AQX A;  3MXB A;  2VBL A;  5E67 A;  4UN9 G;  4UN7 G;  1BP7 A;  3C0W A;  1T9I A;  5A0M B;  2VBN B;  1B24 A;  4UN9 A;  4Z1Z A;  4UN7 A;  5E5O A;  3FD2 A;  3KO2 A;  5AK9 A;  1G9Y A;  4LOX A;  2VS7 A;  2I3Q A;  3QQY A;  4UNC A;  1VDE A;  3HYI A;  3MXB B;  2XE0 B;  1AF5 A;  2VBL B;  4UNA A;  1M5X A;  2VBO B;  2XE0 A;  3E54 A;  5AKN A;  3MIP A;  4UT0 A;  3HYJ A;  1T9J A;  2VBJ A;  4D6O A;  2VBO A;  1G9Z A;  1DQ3 A;  4UN8 G;  1R7M A;  3C0X A;  1DFA A;  5A0W A;  4UN8 A;  4YIT A;  4LQ0 A;  4EFJ A;  1UM2 A;  2VBJ B;  4Z1X A;  4AQU A;  3MX9 A;  2AB5 A;  1JVA A;  4UNB A;  4Z20 A;  2DCH X;  3MIS A;  4AAG A;  2FLD A;  1N3E A;  3OOL A;  5AKM A;  2QOJ Z;  1MOW A;  1LWT A;  2I3P A;  1U0C A;  2O7M A;  1EF0 A;  5A77 A;  2CW7 A;  2EX5 A;  4AAB A;  5A78 A;  3R7P A;  3MXA A;  3EH8 A;  4AAE A;  5E5S A;  4YHX A;  5E63 A;  4AAF A;  5A0M A;  2VBN A;  1P8K Z;  3OOR A;  1N3F A;  5AKF A;  5A72 A;  4YIS A;  4AAD A;  2CW8 A;  3UVF A;  4D6N A; 
#chains in the Genus database with same CATH topology
 1LWS A;  2VS8 A;  1U0D A;  5A74 A;  4AQX A;  3MXB A;  4KZS A;  2VBL A;  5E67 A;  4UN9 G;  4UN7 G;  1BP7 A;  3C0W A;  1T9I A;  5A0M B;  2VBN B;  1B24 A;  4UN9 A;  4Z1Z A;  4UN7 A;  5E5O A;  3FD2 A;  3KO2 A;  5AK9 A;  1G9Y A;  4LOX A;  2VS7 A;  2I3Q A;  3QQY A;  4UNC A;  1VDE A;  3HYI A;  3MXB B;  2XE0 B;  1AF5 A;  2VBL B;  4UNA A;  1M5X A;  2VBO B;  2XE0 A;  3E54 A;  5AKN A;  3MIP A;  4UT0 A;  3HYJ A;  1T9J A;  2VBJ A;  4D6O A;  2VBO A;  1G9Z A;  1DQ3 A;  4UN8 G;  1R7M A;  3C0X A;  1DFA A;  5A0W A;  4UN8 A;  4YIT A;  4LQ0 A;  4EFJ A;  1UM2 A;  2VBJ B;  4Z1X A;  4AQU A;  3MX9 A;  2AB5 A;  1JVA A;  4UNB A;  4Z20 A;  2DCH X;  3MIS A;  4AAG A;  2FLD A;  1N3E A;  3OOL A;  5AKM A;  2QOJ Z;  1MOW A;  1LWT A;  2I3P A;  1U0C A;  2O7M A;  1EF0 A;  5A77 A;  2CW7 A;  2EX5 A;  4AAB A;  5A78 A;  3R7P A;  3MXA A;  3EH8 A;  4AAE A;  5E5S A;  4YHX A;  5E63 A;  4AAF A;  5A0M A;  2VBN A;  1P8K Z;  3OOR A;  2F4L A;  1N3F A;  5AKF A;  5A72 A;  4YIS A;  4AAD A;  2CW8 A;  3UVF A;  4D6N A; 
#chains in the Genus database with same CATH homology
 1LWS A;  2VS8 A;  1U0D A;  5A74 A;  4AQX A;  3MXB A;  2VBL A;  5E67 A;  4UN9 G;  4UN7 G;  1BP7 A;  3C0W A;  1T9I A;  5A0M B;  2VBN B;  1B24 A;  4UN9 A;  4Z1Z A;  4UN7 A;  5E5O A;  3FD2 A;  3KO2 A;  5AK9 A;  1G9Y A;  4LOX A;  2VS7 A;  2I3Q A;  3QQY A;  4UNC A;  1VDE A;  3HYI A;  3MXB B;  2XE0 B;  1AF5 A;  2VBL B;  4UNA A;  1M5X A;  2VBO B;  2XE0 A;  3E54 A;  5AKN A;  3MIP A;  4UT0 A;  3HYJ A;  1T9J A;  2VBJ A;  4D6O A;  2VBO A;  1G9Z A;  1DQ3 A;  4UN8 G;  1R7M A;  3C0X A;  1DFA A;  5A0W A;  4UN8 A;  4YIT A;  4LQ0 A;  4EFJ A;  1UM2 A;  2VBJ B;  4Z1X A;  4AQU A;  3MX9 A;  2AB5 A;  1JVA A;  4UNB A;  4Z20 A;  2DCH X;  3MIS A;  4AAG A;  2FLD A;  1N3E A;  3OOL A;  5AKM A;  2QOJ Z;  1MOW A;  1LWT A;  2I3P A;  1U0C A;  2O7M A;  1EF0 A;  5A77 A;  2CW7 A;  2EX5 A;  4AAB A;  5A78 A;  3R7P A;  3MXA A;  3EH8 A;  4AAE A;  5E5S A;  4YHX A;  5E63 A;  4AAF A;  5A0M A;  2VBN A;  1P8K Z;  3OOR A;  1N3F A;  5AKF A;  5A72 A;  4YIS A;  4AAD A;  2CW8 A;  3UVF A;  4D6N 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...

2I3QA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations