5YLE | KnotProt

5YLEA

Mcr-1 complex with ethanolamine (eta)

Image from the <span class='capital'>rcsb pdb</span> (www.rcsb.org)

Warning

Chain breaks within knot 3₁ (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.

Genus: 126

Slipknot S +3₁

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setting document base to "https://knotprot.cent.uw.edu.pl/view/5yle/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

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APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

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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 script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet1__259377691483897__ 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	29-249	221	1-28	278-331	250-277	28	54	slipknot

Chain Sequence

PKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTS-AYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIRLEHHH

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__259377691483897__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__259377691483897__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/5yle/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__259377691483897__ ready

script 1 started

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Viewer cachePut cache://localLOAD_/static/knot_data/5yle/A/5yle_A.pdb.gz

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/5yle/A/5yle_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/5yle/A/5yle_A.pdb.gz): 724 ms

reading 330 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

330 atoms created

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

Time for creating model: 25 ms

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Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5yle/A/5yle_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5yle/A/5yle_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/5yle/A/5yle_A.pdb.gz): 15 ms

reading 330 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

330 atoms created

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

Time for creating model: 15 ms

Adding embedded #jmolscript: select ({0:329});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

specularPower = 9

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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	2.1	18-247	230	1-17	253-330	248-252	17	78	slipknot
view details	3.1	27-249	223	1-26	276-330	250-275	26	55	slipknot
view details	2.1	13-275	263	1-12	279-330	276-278	12	52	slipknot
view details	2.1	24-275	252		1-13, 277-330	14-23, 276-276	13	54	slipknot
view details	3.1	23-276	254		1-14, 278-330	15-22, 277-277	14	53	slipknot

sequence length	331
structure length	330
publication title	Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance. pubmed doi rcsb
molecule tags	Transferase
molecule keywords	Probable phosphatidylethanolamine transferase Mcr-1
source organism	Escherichia coli
missing residues	70
total genus	Genus: 126
ec nomenclature
pdb deposition date	2017-10-17
KnotProt deposition date	2017-11-08

Image from the rcsb pdb (www.rcsb.org)

5GOVA 5GRRA 5K4PA 5LRMA 5YLEA 5YLFA 5ZJVA 5LRNA
similar chains in the KnotProt database (40% sequence similarity)

6LI4A
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
5GOV A; 5GRR A; 5K4P A; 5LRM A; 5YLE A; 5YLF A; 5ZJV A; 
#similar chains, but unknotted
5LRN A; 
#similar chains in the pdb database (40% sequence similarity)
6LI4 A;

How to cite

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling

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5YLEA

Slipknot S +31

Chain Sequence

Slipknot S +3₁