5CGL | Genus

Total Genus 61

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	61
sequence length	177
structure length	161
Chain Sequence	SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIRLKEALVKIEQMPERTFEEIIAKYVRMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTDDVDNREIIFKGIEQSYYYEGYE

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__0133389370139598__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__0133389370139598__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/5CGL/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__0133389370139598__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"0133389370139598","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/5CGL/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__0133389370139598__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0156433e61c76144eed063/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0156433e61c76144eed063/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0156433e61c76144eed063/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/5d0156433e61c76144eed063/pdb.gz): 89 ms

reading 161 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

161 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:160});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	Transferase
source organism	Neisseria meningitidis
publication title	Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification. pubmed doi rcsb
molecule keywords	Adenosine monophosphate-protein transferase NmFic
total genus	61
structure length	161
sequence length	177
chains with identical sequence	B
ec nomenclature	ec 2.7.7.n1: Protein adenylyltransferase.
pdb deposition date	2015-07-09

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02661	Fic	Fic/DOC family

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.3290.10	Mainly Alpha	Orthogonal Bundle	Fic-like fold	Fido-like domain	5cglA00

4LU4A 4X2CA 2F6SA 4XI8A 4U07A 5CKLA 2VZAA 3ZC7A 5EU0A 3LETA 4U0SA 3ZLMA 3ZCBA 4U0ZA 2G03A 2JK8A 3N3UA 5JJ6A 5JJ7A 2VY3A 5JFFA 5CMTA 5JFZA 3CUCA 4PY3A 3SE5A 4U0UA 5CGLA 3SN9A 4X2EA 4N67A 4NPSA 4WGJA 4X2DA 3S6AA 3SHGA 4U04A 4ITRA 4M16A
chains in the Genus database with same CATH superfamily

4LU4A 4X2CA 2F6SA 4XI8A 4U07A 5CKLA 2VZAA 3ZC7A 5EU0A 3LETA 4U0SA 3ZLMA 3ZCBA 4U0ZA 2G03A 2JK8A 3N3UA 5JJ6A 5JJ7A 2VY3A 5JFFA 2NUNA 5CMTA 5JFZA 3CUCA 4PY3A 3SE5A 4U0UA 5CGLA 1NH1A 3SN9A 4X2EA 4N67A 4NPSA 4WGJA 2NUDA 4X2DA 3S6AA 3SHGA 4U04A 4ITRA 4M16A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4LU4 A;  4X2C A;  2F6S A;  4XI8 A;  4U07 A;  5CKL A;  2VZA A;  3ZC7 A;  5EU0 A;  3LET A;  4U0S A;  3ZLM A;  3ZCB A;  4U0Z A;  2G03 A;  2JK8 A;  3N3U A;  5JJ6 A;  5JJ7 A;  2VY3 A;  5JFF A;  5CMT A;  5JFZ A;  3CUC A;  4PY3 A;  3SE5 A;  4U0U A;  5CGL A;  3SN9 A;  4X2E A;  4N67 A;  4NPS A;  4WGJ A;  4X2D A;  3S6A A;  3SHG A;  4U04 A;  4ITR A;  4M16 A; 
#chains in the Genus database with same CATH topology
 4LU4 A;  4X2C A;  2F6S A;  4XI8 A;  4U07 A;  5CKL A;  2VZA A;  3ZC7 A;  5EU0 A;  3LET A;  4U0S A;  3ZLM A;  3ZCB A;  4U0Z A;  2G03 A;  2JK8 A;  3N3U A;  5JJ6 A;  5JJ7 A;  2VY3 A;  5JFF A;  2NUN A;  5CMT A;  5JFZ A;  3CUC A;  4PY3 A;  3SE5 A;  4U0U A;  5CGL A;  1NH1 A;  3SN9 A;  4X2E A;  4N67 A;  4NPS A;  4WGJ A;  2NUD A;  4X2D A;  3S6A A;  3SHG A;  4U04 A;  4ITR A;  4M16 A; 
#chains in the Genus database with same CATH homology
 4LU4 A;  4X2C A;  2F6S A;  4XI8 A;  4U07 A;  5CKL A;  2VZA A;  3ZC7 A;  5EU0 A;  3LET A;  4U0S A;  3ZLM A;  3ZCB A;  4U0Z A;  2G03 A;  2JK8 A;  3N3U A;  5JJ6 A;  5JJ7 A;  2VY3 A;  5JFF A;  5CMT A;  5JFZ A;  3CUC A;  4PY3 A;  3SE5 A;  4U0U A;  5CGL A;  3SN9 A;  4X2E A;  4N67 A;  4NPS A;  4WGJ A;  4X2D A;  3S6A A;  3SHG A;  4U04 A;  4ITR A;  4M16 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...

5CGLA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations