3PYI | Genus

Total Genus 34

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	34
sequence length	167
structure length	142
Chain Sequence	TSKIALFDQTLIASLLQPLSLNQPDFKAYKTKVKLKISEQRNETSGEKELKFEISRSDDFEFLFSETLNNEKYQILARDHDLTVDFDAFPKVIIQHLLCKNIVPTEINIILDAEKNFCSFELFSKTPISKGKIFSIKLHAVR

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__45288928736522__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__45288928736522__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3PYI/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__45288928736522__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"45288928736522","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3PYI/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__45288928736522__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cffe90fe725ee1fe4aa2f97/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cffe90fe725ee1fe4aa2f97/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cffe90fe725ee1fe4aa2f97/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/5cffe90fe725ee1fe4aa2f97/pdb.gz): 1416 ms

reading 142 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

142 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:141});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

molecule tags	Structural protein
source organism	Caenorhabditis elegans
publication title	Structural basis of the 9-fold symmetry of centrioles. pubmed doi rcsb
molecule keywords	Spindle assembly abnormal protein 6
total genus	34
structure length	142
sequence length	167
chains with identical sequence	B
ec nomenclature
pdb deposition date	2010-12-13

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF16531	SAS-6_N	Centriolar protein SAS N-terminal

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

cath code	Class	Architecture	Topology	Homology	Domain
2.170.210.20	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4; Chain: A, domain 1	Dna Repair Protein Xrcc4; Chain: A, domain 1	3pyiA00

2Y3WA 2Y3VA 4CKPA 3PYIA 4GEXA 4GFCA 4GFAA 3Q0XA 4CKMA 4GEUA 4CKNA 3Q0YA 4G79A
chains in the Genus database with same CATH superfamily

3PYIA 4GFAA 5CJ0A 4GEUA 1IK9A 4GEXA 1FU1A 3Q0XA 4XA4A 4CKMA 3II6A 3SR2A 4CKPA 5CJ4A 5CHXA 3RWRA 4CKNA 2QM4A 4G79A 2Y3WA 2Y3VA 3RWRD 4GFCA 3SR2C 2R9AA 3MUDA 3Q0YA
chains in the Genus database with same CATH topology

2Y3WA 2Y3VA 4CKPA 3PYIA 4GEXA 4GFCA 4GFAA 3Q0XA 4CKMA 4GEUA 4CKNA 3Q0YA 4G79A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2Y3W A;  2Y3V A;  4CKP A;  3PYI A;  4GEX A;  4GFC A;  4GFA A;  3Q0X A;  4CKM A;  4GEU A;  4CKN A;  3Q0Y A;  4G79 A; 
#chains in the Genus database with same CATH topology
 3PYI A;  4GFA A;  5CJ0 A;  4GEU A;  1IK9 A;  4GEX A;  1FU1 A;  3Q0X A;  4XA4 A;  4CKM A;  3II6 A;  3SR2 A;  4CKP A;  5CJ4 A;  5CHX A;  3RWR A;  4CKN A;  2QM4 A;  4G79 A;  2Y3W A;  2Y3V A;  3RWR D;  4GFC A;  3SR2 C;  2R9A A;  3MUD A;  3Q0Y A; 
#chains in the Genus database with same CATH homology
 2Y3W A;  2Y3V A;  4CKP A;  3PYI A;  4GEX A;  4GFC A;  4GFA A;  3Q0X A;  4CKM A;  4GEU A;  4CKN A;  3Q0Y A;  4G79 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...

3PYIA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations