4DH2 | Genus

Total Genus 22

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	22
sequence length	72
structure length	72
Chain Sequence	AVIGDVNADGVVNISDYVLMKRYILRIIADFPADDDMWVGDVNGDNVINDIDCNYLKRYLLHMIREFPKNSY

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__86688511613325__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__86688511613325__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4DH2/B/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__86688511613325__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"86688511613325","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4DH2/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__86688511613325__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d03ac4a54a80bf26d36ade4/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d03ac4a54a80bf26d36ade4/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d03ac4a54a80bf26d36ade4/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/5d03ac4a54a80bf26d36ade4/pdb.gz): 68 ms

reading 72 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

72 atoms created

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

Time for creating model: 15 ms

Adding embedded #jmolscript: select ({0:71});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/protein binding
source organism	Clostridium thermocellum
publication title	Novel Clostridium thermocellum Type I Cohesin-Dockerin Complexes Reveal a Single Binding Mode. pubmed doi rcsb
molecule keywords	Cellulosome anchoring protein cohesin region
total genus	22
structure length	72
sequence length	72
chains with identical sequence	D
ec nomenclature
pdb deposition date	2012-01-27

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	4dh2B00

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

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

4DH2B

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations