4LU4 | Genus

Total Genus 82

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	82
sequence length	220
structure length	220
Chain Sequence	HHMEHNYFYKNSATLKNKHGIKNPRKLYERCAHETAREAVNFRLEPPPGKFDAAYLRTIHWCLFHNTFEWAGVTRDQPFTFEDGSTACMPAMRPKGYKVPFAVGSQIQRELKKLEQRLTAKNNLQGLSRQEFAANAAEVFTALDHAHPFRKGNGRTQRMFMEKLGQAAGYKIDFSLITKERMTYASIEAMQHNNPEPMKDLFEDITHPQKSLLLKEFISQ

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__272879762352461__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__272879762352461__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4LU4/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__272879762352461__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"272879762352461","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4LU4/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__272879762352461__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0071b658d5532c5c8edc3f/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0071b658d5532c5c8edc3f/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0071b658d5532c5c8edc3f/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/5d0071b658d5532c5c8edc3f/pdb.gz): 128 ms

reading 220 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

220 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:219});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	Transferase
source organism	Bartonella quintana
publication title	Crystal Structure of the N-terminal Fic Domain of a Putative Cell Filamentation protein (VirB-translocated Bep effector protein) from Bartonella quintana rcsb
molecule keywords	Putative cell filamentation protein
total genus	82
structure length	220
sequence length	220
chains with identical sequence	B
ec nomenclature
pdb deposition date	2013-07-24

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02661	Fic	Fic/DOC family

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.3290.10	Mainly Alpha	Orthogonal Bundle	Fic-like fold	Fido-like domain	4lu4A00

3SE5A 3N3UA 5JJ6A 2F6SA 5CGLA 4U0UA 4U04A 3ZCBA 4U0SA 5EU0A 4WGJA 4N67A 5CMTA 3ZC7A 2VY3A 5JFFA 5CKLA 5JJ7A 4M16A 3S6AA 4NPSA 3CUCA 3LETA 4X2DA 4ITRA 4LU4A 3ZLMA 4X2EA 4U0ZA 4U07A 5JFZA 4X2CA 3SHGA 4PY3A 2VZAA 2JK8A 4XI8A 2G03A 3SN9A
chains in the Genus database with same CATH superfamily

4XI8A 3N3UA 5JJ6A 3SE5A 2F6SA 2NUNA 5CGLA 4U0UA 4U04A 3ZCBA 4U0SA 5EU0A 4WGJA 4N67A 5CMTA 1NH1A 3ZC7A 2VY3A 5JFFA 5CKLA 5JJ7A 4M16A 3S6AA 4NPSA 3CUCA 3LETA 4X2DA 4ITRA 4LU4A 3ZLMA 4X2EA 4U0ZA 4U07A 5JFZA 4X2CA 3SHGA 4PY3A 2VZAA 2JK8A 2NUDA 2G03A 3SN9A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 3SE5 A;  3N3U A;  5JJ6 A;  2F6S A;  5CGL A;  4U0U A;  4U04 A;  3ZCB A;  4U0S A;  5EU0 A;  4WGJ A;  4N67 A;  5CMT A;  3ZC7 A;  2VY3 A;  5JFF A;  5CKL A;  5JJ7 A;  4M16 A;  3S6A A;  4NPS A;  3CUC A;  3LET A;  4X2D A;  4ITR A;  4LU4 A;  3ZLM A;  4X2E A;  4U0Z A;  4U07 A;  5JFZ A;  4X2C A;  3SHG A;  4PY3 A;  2VZA A;  2JK8 A;  4XI8 A;  2G03 A;  3SN9 A; 
#chains in the Genus database with same CATH topology
 4XI8 A;  3N3U A;  5JJ6 A;  3SE5 A;  2F6S A;  2NUN A;  5CGL A;  4U0U A;  4U04 A;  3ZCB A;  4U0S A;  5EU0 A;  4WGJ A;  4N67 A;  5CMT A;  1NH1 A;  3ZC7 A;  2VY3 A;  5JFF A;  5CKL A;  5JJ7 A;  4M16 A;  3S6A A;  4NPS A;  3CUC A;  3LET A;  4X2D A;  4ITR A;  4LU4 A;  3ZLM A;  4X2E A;  4U0Z A;  4U07 A;  5JFZ A;  4X2C A;  3SHG A;  4PY3 A;  2VZA A;  2JK8 A;  2NUD A;  2G03 A;  3SN9 A; 
#chains in the Genus database with same CATH homology
 3SE5 A;  3N3U A;  5JJ6 A;  2F6S A;  5CGL A;  4U0U A;  4U04 A;  3ZCB A;  4U0S A;  5EU0 A;  4WGJ A;  4N67 A;  5CMT A;  3ZC7 A;  2VY3 A;  5JFF A;  5CKL A;  5JJ7 A;  4M16 A;  3S6A A;  4NPS A;  3CUC A;  3LET A;  4X2D A;  4ITR A;  4LU4 A;  3ZLM A;  4X2E A;  4U0Z A;  4U07 A;  5JFZ A;  4X2C A;  3SHG A;  4PY3 A;  2VZA A;  2JK8 A;  4XI8 A;  2G03 A;  3SN9 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...

4LU4A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations