3R7P | Genus

Total Genus 89

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	89
sequence length	301
structure length	292
Chain Sequence	DNISPWTITGFADAESSFMLTVSKDSKRNTGWSVRPRFRIGLHNKDVTILKSIREYLGAGIITSDIDARIRFESLKELEVVINHFDKYPLITQKRADYLLFKKAFYLIKNKEHLTEEGLNQILTLKASLNLGLSEELKEAFPNTIPAERLLVTGQEIPDSNWVAGFTAGEGSFYIRIAKNSTLKTGYQVQSVFQITQDTRDIELMKNLISYLNCGNIRIRKTCVDLVVTNLNDIKEKIIPFFNKNHIIGVKLQDYRDWCKVVTLIDNKEHLTSEGLEKIQKIKEGMNRGRSL

Loading diagram...

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__32620453129431__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__32620453129431__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3R7P/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__32620453129431__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"32620453129431","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3R7P/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__32620453129431__ 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	Hydrolase/dna
source organism	Leptographium truncatum
publication title	Tapping natural reservoirs of homing endonucleases for targeted gene modification. pubmed doi rcsb
molecule keywords	Ribosomal protein 3/homing endonuclease-like fusion protein
total genus	89
structure length	292
sequence length	301
ec nomenclature	ec 3.1.21.1: Deoxyribonuclease I.
pdb deposition date	2011-03-22

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	3r7pA01
3.10.28.10	Alpha Beta	Roll	Endonuclease I-creI	Homing endonucleases	3r7pA02

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

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

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

3R7PA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations