1V2X | KnotProt

Genus: 61

Knot K +3₁

script 1 started

platformSpeed = 8

JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__635483776090205__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__635483776090205__)

vwrOptions:

{ "name":"jmolApplet1","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/1V2X/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__635483776090205__","codePath":"https:/static/js/j2s/","display":"jmolApplet1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"635483776090205","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/1V2X/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__635483776090205__ 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	99-139	41	1-98, 140-191			98	52	knot

Chain Sequence

MRERTEARRRRIEEVLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQRQRLKAGLYDRPRLDPELYQKVLADW

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__635483776090205__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__635483776090205__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/1V2X/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__635483776090205__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"635483776090205","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/1V2X/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__635483776090205__ ready

script 1 started

platformSpeed = 8

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	98-140	43	1-97, 141-191			97	51	knot
view details	2.1	96-137	42	1-95	143-191	138-142	95	49	slipknot
view details	3.1	99-143	45		1-97, 163-191	98-98, 144-162	97	29	slipknot
view details	2.1	100-145	46		1-98, 162-191	99-99, 146-161	98	30	slipknot
view details	2.1	100-168	69		1-97, 188-191	98-99, 169-187	97	4	slipknot

sequence length	191
structure length	191
publication title	Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme pubmed doi rcsb
molecule tags	Transferase
molecule keywords	tRNA (Gm18) methyltransferase
source organism	Thermus thermophilus
total genus	Genus: 61
ec nomenclature	ec 2.1.1.34: tRNA (guanosine(18)-2'-O)-methyltransferase.
pdb deposition date	2003-10-17
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00588	SpoU_methylase	SpoU rRNA Methylase family

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	1v2xA00

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

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

1ZJRA 4X3LA 4X3MA 7EDCA
similar chains in the KnotProt database (40% sequence similarity)

7OI61 9H1KA 9HCCx 9MUJA 9MUKA
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
1ZJR A; 4X3L A; 4X3M A; 7EDC A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
7OI6 1; 9H1K A; 9HCC x; 9MUJ A; 9MUK A;

1V2XA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁