3QBQ | Genus

Total Genus 29

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	29
sequence length	164
structure length	164
Chain Sequence	CTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSS

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__068305775396182__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__068305775396182__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3QBQ/B/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__068305775396182__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"068305775396182","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3QBQ/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__068305775396182__ ready

script 1 started

platformSpeed = 8

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	Cytokine/cytokine receptor
source organism	Mus musculus
publication title	Structure-based development of a receptor activator of nuclear factor-kappaB ligand (RANKL) inhibitor peptide and molecular basis for osteopetrosis pubmed doi rcsb
molecule keywords	Tumor necrosis factor ligand superfamily member 11
total genus	29
structure length	164
sequence length	164
chains with identical sequence	D
ec nomenclature
pdb deposition date	2011-01-13

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
B	PF00020	TNFR_c6	TNFR/NGFR cysteine-rich region
B	PF18278	RANK_CRD_2	Receptor activator of the NF-KB cysteine-rich repeat domain 2

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

cath code	Class	Architecture	Topology	Homology	Domain
2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A; domain 2	Tumor Necrosis Factor Receptor, subunit A, domain 2	3qbqB02
2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A; domain 2	Tumor Necrosis Factor Receptor, subunit A, domain 2	3qbqB01

3THMF 3ME4A 3TJEF 4MSVB 2X10A 3U3PA 3MI8D 1SG1X 4J6GC 4RSUD 5L36B 3U3VA 5DMJA 1FT4A 2UWIA 3QO4A 4BK4A 4YN0A 4M4PA 1TNRR 4M4RA 3K51B 5CIRE 3U3SA 3FL7A 4FHQA 2HEYR 4KGGC 5IHLA 4MXWR 4BK5A 3WVTA 1ZA3R 1D4VA 3ALQR 3IJ2X 4KGQC 3X3FA 2AW2B 2H9GR 4GIQR 5BNQR 3QD6R 3QBQB 3U3QA 4I9XC 4OD2S 3ME2R 3BUKC 1JMAB 1NCFA 1DU3A 1EXTA 3U3TA 4E4DR 4N90R 3MHDD 3URFZ 2HEVR 3MBWA 1D0GR
chains in the Genus database with same CATH superfamily

3THMF 3ME4A 2E4VA 3TJEF 4MSVB 2X10A 3U3PA 2E4XA 1D0GR 3MI8D 1SG1X 4J6GC 4RSUD 5L36B 3U3VA 5DMJA 1FT4A 2UWIA 3QO4A 4BK4A 4YN0A 4M4PA 1TNRR 4M4RA 3K51B 5CIRE 3U3SA 3FL7A 4FHQA 2HEYR 4KGGC 5IHLA 4MXWR 4BK5A 3WVTA 1ZA3R 1D4VA 3ALQR 3IJ2X 4KGQC 3X3FA 2AW2B 2H9GR 4GIQR 2E4UA 5BNQR 3QD6R 2E4WA 3QBQB 4I9XC 4OD2S 3U3QA 3ME2R 3BUKC 1JMAB 1NCFA 1DU3A 1EXTA 2QR6A 3U3TA 4E4DR 4N90R 3MHDD 3URFZ 2HEVR 3MBWA 2E4YA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 3THM F;  3ME4 A;  3TJE F;  4MSV B;  2X10 A;  3U3P A;  3MI8 D;  1SG1 X;  4J6G C;  4RSU D;  5L36 B;  3U3V A;  5DMJ A;  1FT4 A;  2UWI A;  3QO4 A;  4BK4 A;  4YN0 A;  4M4P A;  1TNR R;  4M4R A;  3K51 B;  5CIR E;  3U3S A;  3FL7 A;  4FHQ A;  2HEY R;  4KGG C;  5IHL A;  4MXW R;  4BK5 A;  3WVT A;  1ZA3 R;  1D4V A;  3ALQ R;  3IJ2 X;  4KGQ C;  3X3F A;  2AW2 B;  2H9G R;  4GIQ R;  5BNQ R;  3QD6 R;  3QBQ B;  3U3Q A;  4I9X C;  4OD2 S;  3ME2 R;  3BUK C;  1JMA B;  1NCF A;  1DU3 A;  1EXT A;  3U3T A;  4E4D R;  4N90 R;  3MHD D;  3URF Z;  2HEV R;  3MBW A;  1D0G R; 
#chains in the Genus database with same CATH topology
 3THM F;  3ME4 A;  2E4V A;  3TJE F;  4MSV B;  2X10 A;  3U3P A;  2E4X A;  1D0G R;  3MI8 D;  1SG1 X;  4J6G C;  4RSU D;  5L36 B;  3U3V A;  5DMJ A;  1FT4 A;  2UWI A;  3QO4 A;  4BK4 A;  4YN0 A;  4M4P A;  1TNR R;  4M4R A;  3K51 B;  5CIR E;  3U3S A;  3FL7 A;  4FHQ A;  2HEY R;  4KGG C;  5IHL A;  4MXW R;  4BK5 A;  3WVT A;  1ZA3 R;  1D4V A;  3ALQ R;  3IJ2 X;  4KGQ C;  3X3F A;  2AW2 B;  2H9G R;  4GIQ R;  2E4U A;  5BNQ R;  3QD6 R;  2E4W A;  3QBQ B;  4I9X C;  4OD2 S;  3U3Q A;  3ME2 R;  3BUK C;  1JMA B;  1NCF A;  1DU3 A;  1EXT A;  2QR6 A;  3U3T A;  4E4D R;  4N90 R;  3MHD D;  3URF Z;  2HEV R;  3MBW A;  2E4Y A; 
#chains in the Genus database with same CATH homology
 3THM F;  3ME4 A;  3TJE F;  4MSV B;  2X10 A;  3U3P A;  3MI8 D;  1SG1 X;  4J6G C;  4RSU D;  5L36 B;  3U3V A;  5DMJ A;  1FT4 A;  2UWI A;  3QO4 A;  4BK4 A;  4YN0 A;  4M4P A;  1TNR R;  4M4R A;  3K51 B;  5CIR E;  3U3S A;  3FL7 A;  4FHQ A;  2HEY R;  4KGG C;  5IHL A;  4MXW R;  4BK5 A;  3WVT A;  1ZA3 R;  1D4V A;  3ALQ R;  3IJ2 X;  4KGQ C;  3X3F A;  2AW2 B;  2H9G R;  4GIQ R;  5BNQ R;  3QD6 R;  3QBQ B;  3U3Q A;  4I9X C;  4OD2 S;  3ME2 R;  3BUK C;  1JMA B;  1NCF A;  1DU3 A;  1EXT A;  3U3T A;  4E4D R;  4N90 R;  3MHD D;  3URF Z;  2HEV R;  3MBW A;  1D0G R;

...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...

3QBQB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations