3B9X | Genus

Total Genus 108

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	108
sequence length	309
structure length	309
Chain Sequence	KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIK

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__143565785949483__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__143565785949483__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3B9X/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__143565785949483__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"143565785949483","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3B9X/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__143565785949483__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfe5c4cd3e461dadcef5e1c/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfe5c4cd3e461dadcef5e1c/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfe5c4cd3e461dadcef5e1c/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/5cfe5c4cd3e461dadcef5e1c/pdb.gz): 580 ms

reading 309 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

309 atoms created

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

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:308});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

publication title	Structural basis for substrate specificity in group I nucleoside hydrolases pubmed doi rcsb
molecule keywords	Pyrimidine-specific ribonucleoside hydrolase rihB
molecule tags	Hydrolase
source organism	Escherichia coli
total genus	108
structure length	309
sequence length	309
chains with identical sequence	B, C, D
ec nomenclature	ec 3.2.2.8: Ribosylpyrimidine nucleosidase.
pdb deposition date	2007-11-07

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01156	IU_nuc_hydro	Inosine-uridine preferring nucleoside hydrolase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase; Chain A	Ribonucleoside hydrolase-like	3b9xA00

3B9GA 1HOZA 4I72A 4KL0A 4I73A 3MKMA 1HP0A 4I70A 4I71A 2MASA 4KPOA 3EPWA 1R4FA 1Q8FA 1KICA 3B9XA 5TSQA 3EPXA 1EZRA 4WR2A 1KIEA 4P5FA 2C40A 4I74A 2FF1A 4KPNA 1MASA 3MKNA 2YHGA 2FF2A 3T8JA 1YOEA 3T8IA 3FZ0A 4I75A 3G5IA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 3B9G A;  1HOZ A;  4I72 A;  4KL0 A;  4I73 A;  3MKM A;  1HP0 A;  4I70 A;  4I71 A;  2MAS A;  4KPO A;  3EPW A;  1R4F A;  1Q8F A;  1KIC A;  3B9X A;  5TSQ A;  3EPX A;  1EZR A;  4WR2 A;  1KIE A;  4P5F A;  2C40 A;  4I74 A;  2FF1 A;  4KPN A;  1MAS A;  3MKN A;  2YHG A;  2FF2 A;  3T8J A;  1YOE A;  3T8I A;  3FZ0 A;  4I75 A;  3G5I A; 
#chains in the Genus database with same CATH topology
 3B9G A;  1HOZ A;  4I72 A;  4KL0 A;  4I73 A;  3MKM A;  1HP0 A;  4I70 A;  4I71 A;  2MAS A;  4KPO A;  3EPW A;  1R4F A;  1Q8F A;  1KIC A;  3B9X A;  5TSQ A;  3EPX A;  1EZR A;  4WR2 A;  1KIE A;  4P5F A;  2C40 A;  4I74 A;  2FF1 A;  4KPN A;  1MAS A;  3MKN A;  2YHG A;  2FF2 A;  3T8J A;  1YOE A;  3T8I A;  3FZ0 A;  4I75 A;  3G5I A; 
#chains in the Genus database with same CATH homology
 3B9G A;  1HOZ A;  4I72 A;  4KL0 A;  4I73 A;  3MKM A;  1HP0 A;  4I70 A;  4I71 A;  2MAS A;  4KPO A;  3EPW A;  1R4F A;  1Q8F A;  1KIC A;  3B9X A;  5TSQ A;  3EPX A;  1EZR A;  4WR2 A;  1KIE A;  4P5F A;  2C40 A;  4I74 A;  2FF1 A;  4KPN A;  1MAS A;  3MKN A;  2YHG A;  2FF2 A;  3T8J A;  1YOE A;  3T8I A;  3FZ0 A;  4I75 A;  3G5I 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...

3B9XA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations