3OXO | Genus

Total Genus 139

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	139
sequence length	480
structure length	469
Chain Sequence	TKFYTDAVEAVKDIPNGATVLVGGFGLCGIPENLIGALLKTGVKELTAVSNNAGVDNFGLGLLLQSKQIKRMISSYVGENAEFERQYLAGELEVELTPQGTLAERIRAGGAGVPAFYTSTGYGTLVQEGGSPIKYNKDGSIAIASKPREVREFNGQHFILEEAIRGDFALVKAWKADQAGNVTFRKSARNFNLPMCKAAETTVVEVEEIVDIGSFAPEDIHIPKIYVHRLVKGEKYEKRIERLSVRKGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGILGLGPYPLQNEVDADLINAGKETVTVLPGASYFSSDESFAMIRGGHVNLTMLGAMQVSKYGDLANWMIPGKLVKGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKAVFDVDRKKGLTLIELWEGLTVDDIKKSTGCDFAVSPKLIPMQQLE

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__991226129039508__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__991226129039508__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3OXO/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__991226129039508__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"991226129039508","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3OXO/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__991226129039508__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cffd423d0d0d4dbe647de53/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cffd423d0d0d4dbe647de53/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cffd423d0d0d4dbe647de53/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/5cffd423d0d0d4dbe647de53/pdb.gz): 1508 ms

reading 469 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

469 atoms created

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

Time for creating model: 31 ms

Adding embedded #jmolscript: select ({0:468});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	Transferase
source organism	Sus scrofa
publication title	Catalytic role of the conformational change in succinyl-CoA:3-oxoacid CoA transferase on binding CoA. pubmed doi rcsb
molecule keywords	Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondr
total genus	139
structure length	469
sequence length	480
chains with identical sequence	B, C, D, E, F, G, H
ec nomenclature	ec 2.8.3.5: 3-oxoacid CoA-transferase.
pdb deposition date	2010-09-21

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01144	CoA_trans	Coenzyme A transferase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.1080.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaconate Coenzyme A-transferase	Glutaconate Coenzyme A-transferase	3oxoA01
3.40.1080.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaconate Coenzyme A-transferase	Glutaconate Coenzyme A-transferase	3oxoA02

2AHUA 1OOYA 1POIB 3D3UA 1POIA 1XR4A 2NRCA 2OASA 3EH7A 1K6DA 2NRBA 3GK7A 2AHWA 3DLXA 1M3EA 5DBNA 5DBNB 4KGBA 2AHVA 1OOZA 3CDKA 3K6MA 3RRLB 1OPEA 3CDKB 3RRLA 3OXOA 3QDQA 1O9LA 2HJ0A
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2AHU A;  1OOY A;  1POI B;  3D3U A;  1POI A;  1XR4 A;  2NRC A;  2OAS A;  3EH7 A;  1K6D A;  2NRB A;  3GK7 A;  2AHW A;  3DLX A;  1M3E A;  5DBN A;  5DBN B;  4KGB A;  2AHV A;  1OOZ A;  3CDK A;  3K6M A;  3RRL B;  1OPE A;  3CDK B;  3RRL A;  3OXO A;  3QDQ A;  1O9L A;  2HJ0 A; 
#chains in the Genus database with same CATH topology
 2AHU A;  1OOY A;  1POI B;  3D3U A;  1POI A;  1XR4 A;  2NRC A;  2OAS A;  3EH7 A;  1K6D A;  2NRB A;  3GK7 A;  2AHW A;  3DLX A;  1M3E A;  5DBN A;  5DBN B;  4KGB A;  2AHV A;  1OOZ A;  3CDK A;  3K6M A;  3RRL B;  1OPE A;  3CDK B;  3RRL A;  3OXO A;  3QDQ A;  1O9L A;  2HJ0 A; 
#chains in the Genus database with same CATH homology
 2AHU A;  1OOY A;  1POI B;  3D3U A;  1POI A;  1XR4 A;  2NRC A;  2OAS A;  3EH7 A;  1K6D A;  2NRB A;  3GK7 A;  2AHW A;  3DLX A;  1M3E A;  5DBN A;  5DBN B;  4KGB A;  2AHV A;  1OOZ A;  3CDK A;  3K6M A;  3RRL B;  1OPE A;  3CDK B;  3RRL A;  3OXO A;  3QDQ A;  1O9L A;  2HJ0 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...

3OXOA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations