4JAL | KnotProt

Genus: 48
Alphaknot: P0AGJ7

Knot K +3₁

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setting document base to "https://knotprot.cent.uw.edu.pl/view/4JAL/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 APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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Jmol getValue SCRIPTCallback null

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language=en_US

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Jmol applet jmolApplet1__280275467136274__ 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	78-120	43	1-77, 121-156			77	36	knot

Chain Sequence

MALNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGYPGAVL

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__280275467136274__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__280275467136274__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/4JAL/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

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Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__280275467136274__ ready

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Viewer cachePut cache://localLOAD_/static/knot_data/4jal/A/4jal_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/4jal/A/4jal_A.pdb.gz

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/4jal/A/4jal_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/4jal/A/4jal_A.pdb.gz): 961 ms

reading 156 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

156 atoms created

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

Time for creating model: 50 ms

Adding embedded #jmolscript: select ({0:155});backbone only;select *;

FileManager.getAtomSetCollectionFromFile(/static/knot_data/4jal/A/4jal_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/4jal/A/4jal_A.pdb.gz): 13 ms

reading 156 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

156 atoms created

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

Time for creating model: 12 ms

Adding embedded #jmolscript: select ({0:155});backbone only;select *;

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Jmol script terminated

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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	78-122	45	1-77, 123-156			77	34	knot
view details	2.1	77-118	42	1-76	124-156	119-123	76	33	slipknot
view details	2.1	81-123	43	124-156	1-77	78-80	77	32	slipknot

sequence length	156
structure length	156
publication title	The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL pubmed doi rcsb
molecule tags	Transferase
molecule keywords	tRNA (cytidine(34)-2'-O)-methyltransferase
source organism	Escherichia coli
total genus	Genus: 48
ec nomenclature	ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
pdb deposition date	2013-02-18
KnotProt deposition date	2014-08-19

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)

1J85A 1MXIA 3N4JA 3N4KA 4JALA 4KDZA 7D51A 7E3QA 7E3SA
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)
1J85 A; 1MXI A; 3N4J A; 3N4K A; 4JAL A; 4KDZ A; 7D51 A; 7E3Q A; 7E3S A; 
#similar chains, but unknotted

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

4JALA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁