3D3U | Genus

Total Genus 117

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	117
sequence length	429
structure length	387
Chain Sequence	QWQELYRQRVCSADEAVVDSLKPGTKVVFGHAAAAPVRFSQAMYRQREKLENITVFHMLYFGDAPHLAPEMRSHVHPTLCHFHEVPELFRQGFFPLDVAVVQVSTPNEEGYCSFGVSCDYTKAAAECAPVVVAEVNKQMPFIGGENLIHISKLTHIIEVDEPIAEVLPGSDLELRIGQNCASLIKDGDTLQLGIGGIPDAVLRALEGHKDLGIHTEMFTDGVMRMIRKGIINGKKKTLHPEKVVTSLIFGSKELYDFVNNNPVIECYPVDYINNPDVIGKNDRMVSINSCLEMDLMGQAGQVDFLRGAKRSKGGISIMAFPSTAKKGTESRIVPILKTGRNEVDYVVTEYGVARLRGATLRQRAEALTAIAHPDFRPALEEEIRRRF

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__801409018708231__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__801409018708231__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3D3U/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__801409018708231__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"801409018708231","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3D3U/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__801409018708231__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfe9aeee2c4c3214bf68dc0/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfe9aeee2c4c3214bf68dc0/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfe9aeee2c4c3214bf68dc0/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/5cfe9aeee2c4c3214bf68dc0/pdb.gz): 66 ms

reading 387 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

387 atoms created

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

Time for creating model: 26 ms

Adding embedded #jmolscript: select ({0:386});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	Porphyromonas gingivalis
publication title	Crystal structure of 4-hydroxybutyrate CoA-transferase (abfT-2) from Porphyromonas gingivalis. rcsb
molecule keywords	4-hydroxybutyrate CoA-transferase
total genus	117
structure length	387
sequence length	429
ec nomenclature
pdb deposition date	2008-05-12

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02550	AcetylCoA_hydro	Acetyl-CoA hydrolase/transferase N-terminal domain
A	PF13336	AcetylCoA_hyd_C	Acetyl-CoA hydrolase/transferase C-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.750.70	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	4-hydroxybutyrate coenzyme like domains	3d3uA02
3.40.1080.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaconate Coenzyme A-transferase	Glutaconate Coenzyme A-transferase	3d3uA01
3.40.1080.20	Alpha Beta	3-Layer(aba) Sandwich	Glutaconate Coenzyme A-transferase	Glutaconate Coenzyme A-transferase	3d3uA03

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

4KGBA 3DJAA 2OASA 1K32A 2NRBA 1VC1A 2NRCA 3MOGA 1FC7A 2DXNA 3D03A 1BPLA 4HYLA 1N6DA 2DXLA 3IH9A 5EUXA 1FC6A 1BUZA 4JC0A 1THNB 3GMFA 4QTPA 5EUWA 1OOYA 1V0FA 1POIA 3IH8A 4L8KA 3K50A 1H4XA 3JU4A 3T6OA 2RRLA 4HIZA 5EUSA 4DGFA 1AUZA 4AE2A 4AEJA 3GK7A 3RRLB 1T6RA 2B78A 1H4YA 3LDFA 1WXWA 3GVJA 3QDQA 4GHNA 5DBNB 5EUUA 1J7XA 2KLNA 3IF5A 1SBOA 2CWWA 1O9LA 3ZXNA 3LKLA 3DORA 3CDKB 3OIRA 3RRLA 1TIDB 1OOZA 3V8VA 3GVLA 2HJ0A 5EUZA 1FC9A 3IHBA 3C0KA 5EZBA 1M3EA 5DBNA 3AGEA 2AHVA 3IHAA 4DGHA 3CDKA 1TH8B 2AS0A 2AHUA 3ZTBA 3OIZA 3V97A 4DMGA 2ZOAA 4XS5A 1POIB 3D3UA 3GHFA 2KA5A 3LLOA 2AHWA 3OXOA 4L1CA 1N6EA 3AGDA 2ZO9B 1XR4A 1WXXA 1H4ZA 3NY7A 3DLXA 1HF2A 1OPEA 1TILB 3F43A 3DUPA 1K6DA 2VY9A 1FCFA 1N6FA 3EH7A 3GVKA 1V0EA 3VSEA 3K6MA 3MGLA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 3GK7 A;  2AHW A;  3OXO A;  3RRL B;  4KGB A;  1M3E A;  2OAS A;  5DBN A;  2NRB A;  2NRC A;  3QDQ A;  2AHV A;  1XR4 A;  5DBN B;  3DLX A;  1OPE A;  3CDK A;  1K6D A;  1O9L A;  1OOY A;  1POI A;  2AHU A;  3EH7 A;  3CDK B;  3RRL A;  1POI B;  3D3U A;  1OOZ A;  2HJ0 A;  3K6M A; 
#chains in the Genus database with same CATH topology
 4KGB A;  3DJA A;  2OAS A;  1K32 A;  2NRB A;  1VC1 A;  2NRC A;  3MOG A;  1FC7 A;  2DXN A;  3D03 A;  1BPL A;  4HYL A;  1N6D A;  2DXL A;  3IH9 A;  5EUX A;  1FC6 A;  1BUZ A;  4JC0 A;  1THN B;  3GMF A;  4QTP A;  5EUW A;  1OOY A;  1V0F A;  1POI A;  3IH8 A;  4L8K A;  3K50 A;  1H4X A;  3JU4 A;  3T6O A;  2RRL A;  4HIZ A;  5EUS A;  4DGF A;  1AUZ A;  4AE2 A;  4AEJ A;  3GK7 A;  3RRL B;  1T6R A;  2B78 A;  1H4Y A;  3LDF A;  1WXW A;  3GVJ A;  3QDQ A;  4GHN A;  5DBN B;  5EUU A;  1J7X A;  2KLN A;  3IF5 A;  1SBO A;  2CWW A;  1O9L A;  3ZXN A;  3LKL A;  3DOR A;  3CDK B;  3OIR A;  3RRL A;  1TID B;  1OOZ A;  3V8V A;  3GVL A;  2HJ0 A;  5EUZ A;  1FC9 A;  3IHB A;  3C0K A;  5EZB A;  1M3E A;  5DBN A;  3AGE A;  2AHV A;  3IHA A;  4DGH A;  3CDK A;  1TH8 B;  2AS0 A;  2AHU A;  3ZTB A;  3OIZ A;  3V97 A;  4DMG A;  2ZOA A;  4XS5 A;  1POI B;  3D3U A;  3GHF A;  2KA5 A;  3LLO A;  2AHW A;  3OXO A;  4L1C A;  1N6E A;  3AGD A;  2ZO9 B;  1XR4 A;  1WXX A;  1H4Z A;  3NY7 A;  3DLX A;  1HF2 A;  1OPE A;  1TIL B;  3F43 A;  3DUP A;  1K6D A;  2VY9 A;  1FCF A;  1N6F A;  3EH7 A;  3GVK A;  1V0E A;  3VSE A;  3K6M A;  3MGL A; 
#chains in the Genus database with same CATH homology
 3GK7 A;  2AHW A;  3OXO A;  3RRL B;  4KGB A;  1M3E A;  2OAS A;  5DBN A;  2NRB A;  2NRC A;  3QDQ A;  2AHV A;  1XR4 A;  5DBN B;  3DLX A;  1OPE A;  3CDK A;  1K6D A;  1O9L A;  1OOY A;  1POI A;  2AHU A;  3EH7 A;  3CDK B;  3RRL A;  1POI B;  3D3U A;  1OOZ A;  2HJ0 A;  3K6M 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...

3D3UA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations