3AI9 | KnotProt

Genus: 64
Alphaknot: Q59034

Knot K +3₁

script 1 started

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JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__045241269137978__ initializing

Jmol getValue debug null

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Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__045241269137978__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/3AI9/X/"

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

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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__045241269137978__ 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	141-182	42	1-140, 183-211			140	29	knot

Chain Sequence

GSHMASMREFIFKANKTITSSDINLKDLPGSCGRLDLLCRCVSDAFFLSHDIRRDVVFYAVLYGQPNPPVCIKFVGSELKKVSPDERNIAIFIKKALKKFEELDEEQRKDWNQSTPGIYVRRLGFRNLVLEKLEEGKNIYYLHMNGEDVENVDIENPVFIIGDHIGIGEEDERFLDEIKAKRISLSPLELHANHCMTMMHNVLDKKRICEI

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__045241269137978__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__045241269137978__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/3AI9/X/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__045241269137978__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"045241269137978","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/3AI9/X/"

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__045241269137978__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/3ai9/X/3ai9_X.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3ai9/X/3ai9_X.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/3ai9/X/3ai9_X.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3ai9/X/3ai9_X.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3ai9/X/3ai9_X.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/3ai9/X/3ai9_X.pdb.gz): 215 ms

reading 211 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

211 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:210});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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3ai9/X/3ai9_X.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/3ai9/X/3ai9_X.pdb.gz): 10 ms

reading 211 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

211 atoms created

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

Time for creating model: 9 ms

Adding embedded #jmolscript: select ({0:210});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

Jmol script terminated

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	140-183	44	1-139, 184-211			139	28	knot

sequence length	211
structure length	211
publication title	Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase pubmed doi rcsb
molecule tags	Transferase
molecule keywords	UPF0217 protein MJ1640
source organism	Methanocaldococcus jannaschii
total genus	Genus: 64
ec nomenclature	ec 2.1.1.257: tRNA (pseudouridine(54)-N(1))-methyltransferase.
pdb deposition date	2010-05-11
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
X	PF04013	Methyltrn_RNA_2	Putative SAM-dependent RNA 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	3ai9X00

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

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

2QMMA 3AIAA
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)
2QMM A; 3AIA A; 
#similar chains, but unknotted

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

3AI9X

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁