6SCF | KnotProt

Genus: 29

Slipknot S +3₁

script 1 started

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JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__37570684341428__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__37570684341428__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/6scf/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:jmolApplet1 (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 jmolApplet1__37570684341428__ ready

Help Knotting data interpretation Full screen

					Knot core range	Knot core length	Knot tails range	Slipknot tails range	Slipknot loops range	N-end length	C-end length	Type
view details				+3₁	5-78	74	1-4	109-113	79-108	4	5	slipknot

Chain Sequence

NKVYLANAFSINMLTKFPTKVVIDKIDRLEFCENIDNEDIINSIGADSTIQLINSLCGTTFQKNRVEIKLEKEDKLYVVQISQRLEEGKILTLEEILKLYESGKVQFFEIIVD

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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__37570684341428__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__37570684341428__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/6scf/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__37570684341428__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"37570684341428","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/6scf/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__37570684341428__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/6scf/A/6scf_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/6scf/A/6scf_A.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/6scf/A/6scf_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/6scf/A/6scf_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/6scf/A/6scf_A.pdb.gz)

The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/static/knot_data/6scf/A/6scf_A.pdb.gz): 1527 ms

reading 113 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

113 atoms created

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

Time for creating model: 50 ms

Adding embedded #jmolscript: select ({0:112});backbone only;select *;

FileManager.getAtomSetCollectionFromFile(/static/knot_data/6scf/A/6scf_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/6scf/A/6scf_A.pdb.gz): 12 ms

reading 113 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

113 atoms created

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

Time for creating model: 10 ms

Adding embedded #jmolscript: select ({0:112});backbone only;select *;

platformSpeed = 7

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

Help Knotoid subchains data interpretation Full screen

					Knot core range	Knot core length	Knot tails range	Slipknot tails range	Slipknot loops range	N-end length	C-end length	Type
view details				3.1	4-78	75	1-3	108-113	79-107	3	6	slipknot
view details				2.1	6-84	79		1-3, 107-113	4-5, 85-106	3	7	slipknot

sequence length	113
structure length	113
publication title	A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate rcsb
molecule tags	Dna
molecule keywords	Uncharacterized protein
source organism	Sulfolobus islandicus rod-shaped virus 1
total genus	Genus: 29
ec nomenclature
pdb deposition date	2019-07-24
KnotProt deposition date	2019-11-06

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF08960	DUF1874	Domain of unknown function (DUF1874)

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

2J85A 2X4IA 1V8OA 1V8PA 2K4BA 4BQQA 5EGPA 6ED6A
similar chains in the KnotProt database (40% sequence similarity)

8EBND
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
2J85 A; 2X4I A; 
#similar chains, but unknotted
6ED6 A; 
#similar chains in the pdb database (40% sequence similarity)
8EBN D;

6SCFA

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁