3T6O | Genus

Total Genus 29

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	29
sequence length	118
structure length	118
Chain Sequence	AMADIRVTHEAQVTVISFPAVFQRLRETEVEQIASTFLAAMQGAQPRKVLIDLEGVEFFGSSFIELLVRGWKRIKEDQQGVFALCSVSPYCVEVLQVTHIDEVWPRYSTKQEALLAMA

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__598821832095344__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__598821832095344__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3T6O/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__598821832095344__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"598821832095344","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3T6O/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__598821832095344__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d03042a7adc6f87bbe482a1/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d03042a7adc6f87bbe482a1/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d03042a7adc6f87bbe482a1/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/5d03042a7adc6f87bbe482a1/pdb.gz): 393 ms

reading 118 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

118 atoms created

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

Time for creating model: 16 ms

Adding embedded #jmolscript: select ({0:117});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	Transport protein
source organism	Planctomyces limnophilus
publication title	The Structure of an Anti-sigma-factor antagonist (STAS) domain protein from Planctomyces limnophilus. rcsb
molecule keywords	Sulfate transporter/antisigma-factor antagonist STAS
total genus	29
structure length	118
sequence length	118
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2011-07-28

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.750.24	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	STAS domain	3t6oA00

4XS5A 3ZXNA 1TH8B 4HYLA 1AUZA 3LLOA 3IH9A 1BUZA 1SBOA 3NY7A 3IF5A 3ZTBA 2KLNA 4DGHA 1TILB 1H4XA 3OIZA 4QTPA 3IHBA 3IHAA 3T6OA 3MGLA 1VC1A 2KA5A 5EUUA 2VY9A 3AGEA 5EUWA 3LKLA 5EZBA 4DGFA 3AGDA 3OIRA 5EUSA 1TIDB 1T6RA 1H4YA 5EUXA 3F43A 3IH8A 1H4ZA 5EUZA 1THNB
chains in the Genus database with same CATH superfamily

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

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

3T6OA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN