2IBP | Genus

Total Genus 153

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	153
sequence length	407
structure length	407
Chain Sequence	EQTVQVKTTGKILQSPCGPIIHGLEDVLIKSTSISDIDGEKGILWYRGYRIEELARLSTYEEVSYLILYGRLPTKRELEDYINRMKKYRELHPATVEVIRNLAKAHPMFALEAAVAAEGAYDEDNQKLIEALSVGRYKAEEKELAYRIAEKLVAKMPTIVAYHYRFSRGLEVVRPRDDLGHAANFLYMMFGREPDPLASRGIDLYLILHADHEVPASTFAAHVVASTLSDLYSSVAAAIAALKGPLHGGANEMAVRNYLEIGTPAKAKEIVEAATKPGGPKLMGVGHRVYKAYDPRAKIFKEFSRDYVAKFGDPQNLFAIASAIEQEVLSHPYFQQRKLYPNVDFWSGIAFYYMGIPYEYFTPIFAMSRVVGWVAHVLEYWENNRIFRPRACYIGPHDLQYIPLEQR

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__8281211289745154__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8281211289745154__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2IBP/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__8281211289745154__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8281211289745154","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2IBP/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__8281211289745154__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd2fdf329a809c5f1328a5/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd2fdf329a809c5f1328a5/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd2fdf329a809c5f1328a5/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/5cfd2fdf329a809c5f1328a5/pdb.gz): 203 ms

reading 407 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

407 atoms created

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

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:406});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	Pyrobaculum aerophilum
publication title	Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. pubmed doi rcsb
molecule keywords	Citrate synthase
total genus	153
structure length	407
sequence length	407
chains with identical sequence	B
ec nomenclature	ec 2.3.3.1: Citrate (Si)-synthase.
pdb deposition date	2006-09-11

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00285	Citrate_synt	Citrate synthase, C-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.230.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450-Terp; domain 2	Cytochrome P450-Terp, domain 2	2ibpA02
1.10.580.10	Mainly Alpha	Orthogonal Bundle	Citrate Synthase; domain 1	Citrate Synthase, domain 1	2ibpA01

1NXGA 1NXEA 2C6XA 4JAGA 4TVMA 5CTSA 1CSHA 1CSSA 1VGMA 1IOMA 1OWCA 1O7XA 2R26A 4JAEA 6CSCA 3HWKA 3CSCA 1IXEA 4E6YA 6CTSA 3O8JA 1AMZA 2CTSA 4XGHA 1AL6A 2H12A 2IFCA 1CTSA 1AJ8A 4JAFA 5CSCA 2R9EA 2CSCA 4YBOA 1A59A 1VGPA 4CTSA 4JADA 2IBPA 3TQGA 5CSCB 3MSUA 4G6BA 2P2WA 1CSCA 4CSCA 1CSRA 1OWBA 3ENJA 1CSIA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1NXG A;  1NXE A;  2C6X A;  4JAG A;  4TVM A;  5CTS A;  1CSH A;  1CSS A;  1VGM A;  1IOM A;  1OWC A;  1O7X A;  2R26 A;  4JAE A;  6CSC A;  3HWK A;  3CSC A;  1IXE A;  4E6Y A;  6CTS A;  3O8J A;  1AMZ A;  2CTS A;  4XGH A;  1AL6 A;  2H12 A;  2IFC A;  1CTS A;  1AJ8 A;  4JAF A;  5CSC A;  2R9E A;  2CSC A;  4YBO A;  1A59 A;  1VGP A;  4CTS A;  4JAD A;  2IBP A;  3TQG A;  5CSC B;  3MSU A;  4G6B A;  2P2W A;  1CSC A;  4CSC A;  1CSR A;  1OWB A;  3ENJ A;  1CSI A; 
#chains in the Genus database with same CATH topology
 1NXG A;  1NXE A;  2C6X A;  4JAG A;  4TVM A;  5CTS A;  1CSH A;  1CSS A;  1VGM A;  1IOM A;  1OWC A;  1O7X A;  2R26 A;  4JAE A;  6CSC A;  3HWK A;  3CSC A;  1IXE A;  4E6Y A;  6CTS A;  3O8J A;  1AMZ A;  2CTS A;  4XGH A;  1AL6 A;  2H12 A;  2IFC A;  1CTS A;  1AJ8 A;  4JAF A;  5CSC A;  2R9E A;  2CSC A;  4YBO A;  1A59 A;  1VGP A;  4CTS A;  4JAD A;  2IBP A;  3TQG A;  5CSC B;  3MSU A;  4G6B A;  2P2W A;  1CSC A;  4CSC A;  1CSR A;  1OWB A;  3ENJ A;  1CSI A; 
#chains in the Genus database with same CATH homology
 1NXG A;  1NXE A;  2C6X A;  4JAG A;  4TVM A;  5CTS A;  1CSH A;  1CSS A;  1VGM A;  1IOM A;  1OWC A;  1O7X A;  2R26 A;  4JAE A;  6CSC A;  3HWK A;  3CSC A;  1IXE A;  4E6Y A;  6CTS A;  3O8J A;  1AMZ A;  2CTS A;  4XGH A;  1AL6 A;  2H12 A;  2IFC A;  1CTS A;  1AJ8 A;  4JAF A;  5CSC A;  2R9E A;  2CSC A;  4YBO A;  1A59 A;  1VGP A;  4CTS A;  4JAD A;  2IBP A;  3TQG A;  5CSC B;  3MSU A;  4G6B A;  2P2W A;  1CSC A;  4CSC A;  1CSR A;  1OWB A;  3ENJ A;  1CSI 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...

2IBPA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations