1TO0 | KnotProt

Genus: 41

Knot K +3₁

script 1 started

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JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__905370349367661__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__905370349367661__)

vwrOptions:

{ "name":"jmolApplet1","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/1TO0/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__905370349367661__","codePath":"https:/static/js/j2s/","display":"jmolApplet1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"905370349367661","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/1TO0/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__905370349367661__ 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	75-124	50	1-74, 125-157			74	33	knot

Chain Sequence

MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEK---------MKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPY

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__905370349367661__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__905370349367661__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/1TO0/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__905370349367661__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"905370349367661","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/1TO0/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__905370349367661__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/1to0/A/1to0_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1to0/A/1to0_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1to0/A/1to0_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/1to0/A/1to0_A.pdb.gz): 998 ms

reading 148 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

148 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:147});backbone only;select *;

Viewer cachePut cache://localLOAD_/static/knot_data/1to0/A/1to0_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1to0/A/1to0_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1to0/A/1to0_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/1to0/A/1to0_A.pdb.gz): 10 ms

reading 148 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

148 atoms created

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

Time for creating model: 8 ms

Adding embedded #jmolscript: select ({0:147});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	66-116	51	1-65, 117-148			65	32	knot
view details	2.1	63-113	51	1-62	119-148	114-118	62	30	slipknot
view details	2.1	67-125	59		1-65, 135-148	66-66, 126-134	65	14	slipknot
view details	2.1	67-134	68		1-65, 143-148	66-66, 135-142	65	6	slipknot

sequence length	157
structure length	148
publication title	X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis rcsb
molecule tags	Structural genomics, unknown function
molecule keywords	Hypothetical UPF0247 protein yyda
source organism	Bacillus subtilis
missing residues	43-51
total genus	Genus: 41
ec nomenclature	ec 2.1.1.177: 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase.
pdb deposition date	2004-06-11
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02590	SPOUT_MTase	Predicted SPOUT methyltransferase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	1to0A00

1UAMA 3AIAA 3NK7A 3KNUA 1J85A 2HA8A 4IG6A 3DCMX 1TO0A 1O6DA 2I6DA 1NXZA 3L8UA 1X7OA 1VH0A 1GZ0A 1MXIA 1V6ZA 4FAKA 4H3YA 3E5YA 4CNGB 1K3RA 2O3AA 3ILKA 1ZJRA 2CX8A 3N4KA 1P9PA 1VHYA 4H3ZA 3IEFA 1VHKA 1X7PA 2QMMA 3N4JA 2QWVA 2YY8A 4CNFB 4CNEB 3QUVA 2Z0YA 1NS5A 3KTYA 3KY7A 3GYQA 3AXZA 3AI9X 3NK6A 4E8BA 1UALA 1UAKA 1V2XA 3ONPA 3IC6A 1UAJA
chains in the KnotProt database with same CATH superfamily

#chains in the KnotProt database with same CATH superfamily
 1UAM A;  3AIA A;  3NK7 A;  3KNU A;  1J85 A;  2HA8 A;  4IG6 A;  3DCM X;  1TO0 A;  1O6D A;  2I6D A;  1NXZ A;  3L8U A;  1X7O A;  1VH0 A;  1GZ0 A;  1MXI A;  1V6Z A;  4FAK A;  4H3Y A;  3E5Y A;  4CNG B;  1K3R A;  2O3A A;  3ILK A;  1ZJR A;  2CX8 A;  3N4K A;  1P9P A;  1VHY A;  4H3Z A;  3IEF A;  1VHK A;  1X7P A;  2QMM A;  3N4J A;  2QWV A;  2YY8 A;  4CNF B;  4CNE B;  3QUV A;  2Z0Y A;  1NS5 A;  3KTY A;  3KY7 A;  3GYQ A;  3AXZ A;  3AI9 X;  3NK6 A;  4E8B A;  1UAL A;  1UAK A;  1V2X A;  3ONP A;  3IC6 A;  1UAJ A; 
#chains in the KnotProt database with same CATH topology
 1UAM A;  3AIA A;  3NK7 A;  3KNU A;  1J85 A;  2HA8 A;  4IG6 A;  3DCM X;  1TO0 A;  1O6D A;  2I6D A;  1NXZ A;  3L8U A;  1X7O A;  1VH0 A;  1GZ0 A;  1MXI A;  1V6Z A;  4FAK A;  4H3Y A;  3E5Y A;  4CNG B;  1K3R A;  2O3A A;  3ILK A;  1ZJR A;  2CX8 A;  3N4K A;  1P9P A;  1VHY A;  4H3Z A;  3IEF A;  1VHK A;  1X7P A;  2QMM A;  3N4J A;  2QWV A;  2YY8 A;  4CNF B;  4CNE B;  3QUV A;  2Z0Y A;  1NS5 A;  3KTY A;  3KY7 A;  3GYQ A;  3AXZ A;  3AI9 X;  3NK6 A;  4E8B A;  1UAL A;  1UAK A;  1V2X A;  3ONP A;  3IC6 A;  1UAJ A; 
#chains in the KnotProt database with same CATH homology
 1UAM A;  3AIA A;  3NK7 A;  3KNU A;  1J85 A;  2HA8 A;  4IG6 A;  3DCM X;  1TO0 A;  1O6D A;  2I6D A;  1NXZ A;  3L8U A;  1X7O A;  1VH0 A;  1GZ0 A;  1MXI A;  1V6Z A;  4FAK A;  4H3Y A;  3E5Y A;  4CNG B;  1K3R A;  2O3A A;  3ILK A;  1ZJR A;  2CX8 A;  3N4K A;  1P9P A;  1VHY A;  4H3Z A;  3IEF A;  1VHK A;  1X7P A;  2QMM A;  3N4J A;  2QWV A;  2YY8 A;  4CNF B;  4CNE B;  3QUV A;  2Z0Y A;  1NS5 A;  3KTY A;  3KY7 A;  3GYQ A;  3AXZ A;  3AI9 X;  3NK6 A;  4E8B A;  1UAL A;  1UAK A;  1V2X A;  3ONP A;  3IC6 A;  1UAJ A;

1VH0A 4FAKA
similar chains in the KnotProt database (40% sequence similarity)

None
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
1VH0 A; 4FAK A; 
#similar chains, but unknotted

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

1TO0A

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁