5X9R | KnotProt

5X9RA

Structural insights into the elevator-like mechanism of the sodium/citrate symporter cits

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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 156

Slipknot S +3₁

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setting document base to "https://knotprot.cent.uw.edu.pl/view/5x9r/A/"

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

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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 MEASURECallback 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 applet jmolApplet1__759796945351759__ 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	194-389	196	1-193	399-425	390-398	193	27	slipknot

Chain Sequence

FKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFIIGAIFGEIGKRLPIFNKYIGGAPVMIFLVAAYFVYAGIFTQKEIDAISNVMDKSNFLNLFIAVLITGAILSVNRRLLLKSLLGYIPTILMGIVGASIFGIAIGLVFGIPVDRIMMLYVLPIMGGGNGAGAVPLSEIYHSVTGRSREEYYSTAIAILTIANIFAIVFAAVLDIIGKKHTWLSGEGELVR---------EKTGQITHRETAVGLVLSTTCFLLAYVVAKKILPSIGGVAIHYFAWMVLIVAALNASGLCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIINAITFANVVIAAIIVIGAVLGAAIGGWLMGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLISYAQISSRLGGGIVLVIASIVFGMM

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__759796945351759__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__759796945351759__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/5x9r/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__759796945351759__ ready

script 1 started

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Viewer cachePut cache://localLOAD_/static/knot_data/5x9r/A/5x9r_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5x9r/A/5x9r_A.pdb.gz

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Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5x9r/A/5x9r_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5x9r/A/5x9r_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/5x9r/A/5x9r_A.pdb.gz): 442 ms

reading 416 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

416 atoms created

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

Time for creating model: 48 ms

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loadScript /static/js/j2s/J/render/MeshRenderer.js

loadScript /static/js/j2s/J/shape/Mesh.js

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5x9r/A/5x9r_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/5x9r/A/5x9r_A.pdb.gz): 16 ms

reading 416 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

416 atoms created

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

Time for creating model: 16 ms

Adding embedded #jmolscript: select ({0:415});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	61-374	314	1-60	395-416	375-394	60	22	slipknot
view details	2.1	66-380	315		1-62, 385-416	63-65, 381-384	62	32	slipknot
view details	2.1	71-378	308		1-63, 391-416	64-70, 379-390	63	26	slipknot
view details	2.1	104-374	271		1-65, 395-416	66-103, 375-394	65	22	slipknot
view details	2.1	100-361	262		1-95, 366-416	96-99, 362-365	95	51	slipknot
view details	2.1	103-359	257		1-99, 364-416	100-102, 360-363	99	53	slipknot
view details	2.3	112-387	276		1-106, 393-416	107-111, 388-392	106	24	slipknot
view details	2.1	125-377	253		1-113, 391-416	114-124, 378-390	113	26	slipknot
view details	2.1	132-384	253		1-128, 390-416	129-131, 385-389	128	27	slipknot
view details	2.1	167-375	209		1-133, 394-416	134-166, 376-393	133	23	slipknot

sequence length	425
structure length	416
publication title	Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS pubmed doi rcsb
molecule tags	Transport protein
molecule keywords	Citrate-sodium symporter
source organism	Klebsiella pneumoniae
missing residues	229-237
total genus	Genus: 156
ec nomenclature
pdb deposition date	2017-03-08
KnotProt deposition date	2017-06-23

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

5XARA 5XASA 5XATA
similar chains in the KnotProt database (40% sequence similarity)

5A1SA 9LSHA 9LSIA 9LSJA 9LSKA
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
5XAR A; 5XAS A; 5XAT A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
5A1S A; 9LSH A; 9LSI A; 9LSJ A; 9LSK A;

How to cite

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling

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5X9RA

Slipknot S +31

Chain Sequence

Slipknot S +3₁