3VEJ | Genus

Total Genus 13

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	13
sequence length	40
structure length	40
Chain Sequence	VDLTVPWDDIEALLKNNFENDQAAVRQVMERLQKGWSLAK

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__636832917091254__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__636832917091254__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3VEJ/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__636832917091254__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"636832917091254","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3VEJ/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__636832917091254__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0345b0faf1fe93d6bffb77/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0345b0faf1fe93d6bffb77/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0345b0faf1fe93d6bffb77/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/5d0345b0faf1fe93d6bffb77/pdb.gz): 674 ms

reading 40 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

40 atoms created

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

Time for creating model: 14 ms

Adding embedded #jmolscript: select ({0:39});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

publication title	Get5 Carboxyl-terminal Domain Is a Novel Dimerization Motif That Tethers an Extended Get4/Get5 Complex. pubmed doi rcsb
molecule keywords	Ubiquitin-like protein MDY2
molecule tags	Protein binding
source organism	Saccharomyces cerevisiae
total genus	13
structure length	40
sequence length	40
chains with identical sequence	B
ec nomenclature
pdb deposition date	2012-01-08

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.286.70	Mainly Alpha	Orthogonal Bundle	GTP Cyclohydrolase I; Chain A, domain 1	GTP Cyclohydrolase I; Chain A, domain 1	3vejA00

2LO0A 2LNZA 3VEJA
chains in the Genus database with same CATH superfamily

1N3RA 1A9CA 2WSEK 1FBXA 1GTPA 1WM9A 1WURA 4E45B 3LW5K 2WSEG 1N3TA 3BMBA 4E44B 1FB1A 5DMZA 3LW5G 4JA3A 1EFUB 4DU6A 2O01G 1EL6A 3B0BC 1IS8A 1A8RA 1TFEA 4R8QA 4DRBJ 1N3SA 1IS7A 2PN0A 1WPLA 2LNZA 2P11A 4Q7JA 2WSCK 2KR1A 1WUQA 2WSFK 4QPMA 1AIPC 3VEJA 2LO0A 4NE3B 2WSCG 2WSFG 4NE6B 4DRAE 4NE5B
chains in the Genus database with same CATH topology

1N3RA 1A9CA 1FBXA 1GTPA 1WM9A 1WURA 4E45B 1N3TA 3BMBA 4E44B 1FB1A 5DMZA 4JA3A 1EFUB 4DU6A 1EL6A 3B0BC 1IS8A 1A8RA 1TFEA 4R8QA 4DRBJ 1N3SA 1IS7A 2PN0A 1WPLA 2LNZA 2P11A 4Q7JA 2KR1A 1WUQA 4QPMA 1AIPC 3VEJA 2LO0A 4NE3B 4NE6B 4DRAE 4NE5B
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2LO0 A;  2LNZ A;  3VEJ A; 
#chains in the Genus database with same CATH topology
 1N3R A;  1A9C A;  2WSE K;  1FBX A;  1GTP A;  1WM9 A;  1WUR A;  4E45 B;  3LW5 K;  2WSE G;  1N3T A;  3BMB A;  4E44 B;  1FB1 A;  5DMZ A;  3LW5 G;  4JA3 A;  1EFU B;  4DU6 A;  2O01 G;  1EL6 A;  3B0B C;  1IS8 A;  1A8R A;  1TFE A;  4R8Q A;  4DRB J;  1N3S A;  1IS7 A;  2PN0 A;  1WPL A;  2LNZ A;  2P11 A;  4Q7J A;  2WSC K;  2KR1 A;  1WUQ A;  2WSF K;  4QPM A;  1AIP C;  3VEJ A;  2LO0 A;  4NE3 B;  2WSC G;  2WSF G;  4NE6 B;  4DRA E;  4NE5 B; 
#chains in the Genus database with same CATH homology
 1N3R A;  1A9C A;  1FBX A;  1GTP A;  1WM9 A;  1WUR A;  4E45 B;  1N3T A;  3BMB A;  4E44 B;  1FB1 A;  5DMZ A;  4JA3 A;  1EFU B;  4DU6 A;  1EL6 A;  3B0B C;  1IS8 A;  1A8R A;  1TFE A;  4R8Q A;  4DRB J;  1N3S A;  1IS7 A;  2PN0 A;  1WPL A;  2LNZ A;  2P11 A;  4Q7J A;  2KR1 A;  1WUQ A;  4QPM A;  1AIP C;  3VEJ A;  2LO0 A;  4NE3 B;  4NE6 B;  4DRA E;  4NE5 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...

3VEJA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization