1OHZ | Genus

Total Genus 18

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	18
sequence length	56
structure length	56
Chain Sequence	GDVNGDGTINSTDLTMLKRSVLRAITLTDDAKARADVDKNGSINSTDVLLLSRYLL

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__428537596775307__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__428537596775307__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1OHZ/B/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__428537596775307__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"428537596775307","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1OHZ/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__428537596775307__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfbbb472d5d85c0cbfb4cdc/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfbbb472d5d85c0cbfb4cdc/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfbbb472d5d85c0cbfb4cdc/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/5cfbbb472d5d85c0cbfb4cdc/pdb.gz): 347 ms

reading 56 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

56 atoms created

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

Time for creating model: 14 ms

Adding embedded #jmolscript: select ({0:55});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	Cell adhesion
source organism	Clostridium thermocellum
publication title	Cellulosome Assembly Revealed by the Crystal Structure of the Cohesin-Dockerin Complex pubmed doi rcsb
molecule keywords	CELLULOSOMAL SCAFFOLDING PROTEIN A
total genus	18
structure length	56
sequence length	56
ec nomenclature	ec 3.2.1.8: Endo-1,4-beta-xylanase.
pdb deposition date	2003-06-04

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
B	PF00404	Dockerin_1	Dockerin type I domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.1330.10	Mainly Alpha	Orthogonal Bundle	Type 1 dockerin domain	Dockerin domain	1ohzB00

1DAQA 2JNKA 4FL4C 1OHZB 4IU2B 1DAVA 4UYQB 2CCLB 3KCPA 4DH2B 5LXVB 4U3SB 4WI0B 5K39B 4WKZA 2Y3NB 2B59B 4FL4A 4UYPB 5G5DB 2VN6B 3UL4B 2VN5B 2OZNB 2MTEA 4IU3B
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1DAQ A;  2JNK A;  4FL4 C;  1OHZ B;  4IU2 B;  1DAV A;  4UYQ B;  2CCL B;  3KCP A;  4DH2 B;  5LXV B;  4U3S B;  4WI0 B;  5K39 B;  4WKZ A;  2Y3N B;  2B59 B;  4FL4 A;  4UYP B;  5G5D B;  2VN6 B;  3UL4 B;  2VN5 B;  2OZN B;  2MTE A;  4IU3 B; 
#chains in the Genus database with same CATH topology
 1DAQ A;  2JNK A;  4FL4 C;  1OHZ B;  4IU2 B;  1DAV A;  4UYQ B;  2CCL B;  3KCP A;  4DH2 B;  5LXV B;  4U3S B;  4WI0 B;  5K39 B;  4WKZ A;  2Y3N B;  2B59 B;  4FL4 A;  4UYP B;  5G5D B;  2VN6 B;  3UL4 B;  2VN5 B;  2OZN B;  2MTE A;  4IU3 B; 
#chains in the Genus database with same CATH homology
 1DAQ A;  2JNK A;  4FL4 C;  1OHZ B;  4IU2 B;  1DAV A;  4UYQ B;  2CCL B;  3KCP A;  4DH2 B;  5LXV B;  4U3S B;  4WI0 B;  5K39 B;  4WKZ A;  2Y3N B;  2B59 B;  4FL4 A;  4UYP B;  5G5D B;  2VN6 B;  3UL4 B;  2VN5 B;  2OZN B;  2MTE A;  4IU3 B;

...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...

1OHZB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations