4P5F | Genus

Total Genus 125

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	125
sequence length	367
structure length	355
Chain Sequence	LTPTEAAVLRELRLHRPQLPLDTLLFTDPNKDPDDVVTYTIAKQLQADGFLRLTDVVVTLGDADMRSQRAQLAKGVFDRLALPDVRVARGQDYPMTSTQAREHSKFLAEGAALRAAPDAVHTDGVRAMCERLATSPHKLGMVVIAGMTDASALLAEAGDLVREKVASITIMGGIDPARDADGLVQPDTRAYNNATDIHAARALYRRAQQLGIPLRILTKEAAYKAAVPPAFYEGIARNGHPVGEYLRDVQKNALKGLWEGIQANLIPGLDTAWFFRTFVAGALSFDAIWPQVTKLNLYDPLTLLAALPGTARLLFQPTPMHREGASPVEHVGHAEVVRPEKARLLLSALAKAALV

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__891803206209526__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__891803206209526__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4P5F/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__891803206209526__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"891803206209526","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4P5F/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__891803206209526__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d008f7c2af9fbe3f097557a/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d008f7c2af9fbe3f097557a/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d008f7c2af9fbe3f097557a/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/5d008f7c2af9fbe3f097557a/pdb.gz): 1004 ms

reading 355 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

355 atoms created

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

Time for creating model: 26 ms

Adding embedded #jmolscript: select ({0:354});backbone only;select *;

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	The crystal structure of type III effector protein XopQ from Xanthomonas oryzae complexed with adenosine diphosphate ribose. pubmed doi rcsb
molecule keywords	Inosine-uridine nucleoside N-ribohydrolase
molecule tags	Hydrolase
source organism	Xanthomonas oryzae pv. oryzae
total genus	125
structure length	355
sequence length	367
chains with identical sequence	B
ec nomenclature
pdb deposition date	2014-03-17

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	4p5fA00

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

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

4P5FA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations