3O2R | Genus

Total Genus 60

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	60
sequence length	144
structure length	142
Chain Sequence	NIEKLEQSLTYEFKDKNLLIHALTHKSFKSYNNERLEFLGDAVLDLVVGEYLFHKFAKDAEGDLSKLRAALVNEKSFAKIANSLNLGDFILMSVAEENNGGKEKPSILSDALEAIIGAIHLEAGFEFAKTIALRLIEKNFPI

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__1982094098604059__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__1982094098604059__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3O2R/B/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__1982094098604059__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"1982094098604059","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3O2R/B/"

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__1982094098604059__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cffbee5c1298f547ea89015/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cffbee5c1298f547ea89015/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cffbee5c1298f547ea89015/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/5cffbee5c1298f547ea89015/pdb.gz): 780 ms

reading 142 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

142 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:141});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
source organism	Campylobacter jejuni subsp. jejuni
publication title	Structural Flexibility in Region Involved in Dimer Formation of Nuclease Domain of Ribonuclase III (rnc) from Campylobacter jejuni. rcsb
molecule keywords	Ribonuclease III
total genus	60
structure length	142
sequence length	144
chains with identical sequence	D
ec nomenclature	ec 3.1.26.3: Ribonuclease III.
pdb deposition date	2010-07-22

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
B	PF14622	Ribonucleas_3_3	Ribonuclease-III-like

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.1520.10	Mainly Alpha	Orthogonal Bundle	Ribonuclease iii, N-terminal Endonuclease Domain; Chain A	Ribonuclease III domain	3o2rB00

1O0WA 2GSLA 3RV1A 3O2RB 1YZ9A 2FFLA 2EZ6A 4M2ZA 3C4BA 1YYOA 1YYWA 2NUGA 2EB1A 1RC7A 4OUNA 1U61A 2QVWA 1I4SA 3O2RA 2A11A 3N3WA 1RC5A 3C4TA 1JFZA 3RV0A 2NUFA 4OOGC 2NUEA 1YYKA 4M30A
chains in the Genus database with same CATH superfamily

1ZTDA 1O0WA 2GSLA 3RV1A 3O2RB 1YZ9A 2FFLA 2EZ6A 4M2ZA 3C4BA 1YYOA 1YYWA 2NUGA 2EB1A 1RC7A 4OUNA 1U61A 2QVWA 1I4SA 3O2RA 2A11A 3N3WA 1RC5A 3C4TA 1JFZA 3RV0A 2NUFA 4OOGC 2NUEA 1YYKA 4M30A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1O0W A;  2GSL A;  3RV1 A;  3O2R B;  1YZ9 A;  2FFL A;  2EZ6 A;  4M2Z A;  3C4B A;  1YYO A;  1YYW A;  2NUG A;  2EB1 A;  1RC7 A;  4OUN A;  1U61 A;  2QVW A;  1I4S A;  3O2R A;  2A11 A;  3N3W A;  1RC5 A;  3C4T A;  1JFZ A;  3RV0 A;  2NUF A;  4OOG C;  2NUE A;  1YYK A;  4M30 A; 
#chains in the Genus database with same CATH topology
 1ZTD A;  1O0W A;  2GSL A;  3RV1 A;  3O2R B;  1YZ9 A;  2FFL A;  2EZ6 A;  4M2Z A;  3C4B A;  1YYO A;  1YYW A;  2NUG A;  2EB1 A;  1RC7 A;  4OUN A;  1U61 A;  2QVW A;  1I4S A;  3O2R A;  2A11 A;  3N3W A;  1RC5 A;  3C4T A;  1JFZ A;  3RV0 A;  2NUF A;  4OOG C;  2NUE A;  1YYK A;  4M30 A; 
#chains in the Genus database with same CATH homology
 1O0W A;  2GSL A;  3RV1 A;  3O2R B;  1YZ9 A;  2FFL A;  2EZ6 A;  4M2Z A;  3C4B A;  1YYO A;  1YYW A;  2NUG A;  2EB1 A;  1RC7 A;  4OUN A;  1U61 A;  2QVW A;  1I4S A;  3O2R A;  2A11 A;  3N3W A;  1RC5 A;  3C4T A;  1JFZ A;  3RV0 A;  2NUF A;  4OOG C;  2NUE A;  1YYK A;  4M30 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...

3O2RB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations