3ILK | KnotProt

Genus: 73

Knot K +3₁

script 1 started

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AppletRegistry.checkIn(jmolApplet1__084127675535553__)

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

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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

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Jmol getValue SCRIPTCallback null

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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__084127675535553__ 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	80-130	51	1-79, 131-240			79	110	knot

Chain Sequence

NAMLENIRIVLIETSHSGNIGSAARAMKTMGLTQLCLVSPKSVDEQSYALSAGAENIVKNARVVDSFDEAVDDCSLVIGTSARLRHLQNTLIEPRECAEKVVAYKGKIAIVFGRERIGLTNEELLKCHYHLNIPANPDYSSLNLAMAVQLVSYELRMAFLVQNNKKNSLSL-EKNYPTTDQLAYFFDYTERIYQSLGFIQNQGVMRKLKRLYYRAKLEKNELNILNGMLSAVEKRIDLTK

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__084127675535553__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__084127675535553__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/3ilk/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__084127675535553__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/3ilk/A/3ilk_A.pdb.gz

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

Viewer cachePut cache://localLOAD_/static/knot_data/3ilk/A/3ilk_A.pdb.gz

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3ilk/A/3ilk_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/3ilk/A/3ilk_A.pdb.gz): 696 ms

reading 239 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

239 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:238});backbone only;select *;

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cartoonsFancy = true

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traceAlpha = true

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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/3ilk/A/3ilk_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/3ilk/A/3ilk_A.pdb.gz): 11 ms

reading 239 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

239 atoms created

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

Time for creating model: 10 ms

Adding embedded #jmolscript: select ({0:238});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	79-131	53	1-78, 132-239			78	108	knot
view details	2.1	81-165	85		1-78, 183-239	79-80, 166-182	78	57	slipknot
view details	2.1	81-182	102		1-78, 206-239	79-80, 183-205	78	34	slipknot

sequence length	240
structure length	239
publication title	The structure of a probable methylase family protein from Haemophilus influenzae Rd KW20 rcsb
molecule tags	Structural genomics, unknown function
molecule keywords	Uncharacterized tRNA/rRNA methyltransferase HI0380
source organism	Haemophilus influenzae
missing residues	172
total genus	Genus: 73
ec nomenclature	ec 2.1.1.-:
pdb deposition date	2009-08-07
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	3ilkA01

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

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

3IC6A 3KTYA 4CNDA 4CNEA 4XBOA 5GM8A 5GMBA 5GMCA
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)
3IC6 A; 3KTY A; 4CND A; 4CNE A; 4XBO A; 5GM8 A; 5GMB A; 5GMC A; 
#similar chains, but unknotted

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

3ILKA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁