3AIA | KnotProt

Genus: 69
Alphaknot: Q59034

Knot K +3₁

script 1 started

platformSpeed = 8

JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__632149592862694__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__632149592862694__)

vwrOptions:

{ "name":"jmolApplet1","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/3AIA/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__632149592862694__","codePath":"https:/static/js/j2s/","display":"jmolApplet1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"632149592862694","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/3AIA/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__632149592862694__ 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	135-176	42	1-134, 177-200			134	24	knot

Chain Sequence

MREFIFKANKTITSSDINLKDLPGSCGRLDLLCRCVSDAFFLSHDIRRDVVFYAVLYGQPNPPVCIKFVGSELKKVSPDERNIAIFIKKALKKFEELDEEQRKDWNQSTPGIYVRRLGFRNLVLEKLEEGKNIYYLHMNGEDVENVDIENPVFIIGDHIGIGEEDERFLDEIKAKRISLSPLELHANHCITIIHNVLDKK

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__632149592862694__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__632149592862694__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/3AIA/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__632149592862694__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"632149592862694","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/3AIA/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__632149592862694__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/3aia/A/3aia_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3aia/A/3aia_A.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/3aia/A/3aia_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3aia/A/3aia_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3aia/A/3aia_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/3aia/A/3aia_A.pdb.gz): 319 ms

reading 200 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

200 atoms created

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

Time for creating model: 38 ms

Adding embedded #jmolscript: select ({0:199});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/3aia/A/3aia_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/3aia/A/3aia_A.pdb.gz): 16 ms

reading 200 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

200 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:199});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	134-177	44	1-133, 178-200			133	23	knot
view details				3.1	135-178	44		1-133, 196-200	134-134, 179-195	133	5	slipknot

sequence length	200
structure length	200
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: 69
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
A	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	3aiaA00

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

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

...loading similar chains, please wait...
similar chains in the KnotProt database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the KnotProt 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...

3AIAA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁