4NWX | KnotProt

Genus: 194

Slipknot S +3₁

script 1 started

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Jmol JavaScript applet jmolApplet1__988922976676775__ initializing

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

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Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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language=en_US

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Jmol applet jmolApplet1__988922976676775__ 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	7-437	431	1-6	460-503	438-459	6	44	slipknot

Chain Sequence

KKPTALIILDGFANRESEHGNAVKLANKPNFDRYYNKYPTTQIEASGLDVGLPEGQMGNSEVGHMNIGAGRIVYQSLTRINKSIEDGDFFENDVLNNAIAHVNSHDSALHIFGLLSDGGVHSHYKHLFALLELAKKQGVEKVYVHAFLDGRDVDQKSALKYIEETEAKFNELGIGQFASVSGRYYAMDRDKRWEREEKAYNAIRNFDAPTYATAKEGVEASYNEGLTDEFVVPFIVENQNDGVNDGDAVIFYNFRPDRAAQLSEIFANRAFEGFKVEQVKDLFYATFTKYNDNIDAAIVFEKVDLNNTIGEIAQNNNLTQLRIAETEKYPHVTYFMSGGRNEEFKGERRRLIDSPKVATYDLKPEMSAYEVKDALLEELNKGDLDLIILNFANPDMVGHSGMLEPTIKAIEAVDECLGEVVDKILDMDGYAIITADHGNSDQVLTDDDQPMTTHTTNPVPVIVTKEGVTLRETGRLGDLAPTLLDLLNVEQPEDMTGESLIKH

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__988922976676775__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__988922976676775__)

vwrOptions:

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

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Jmol applet jmolApplet0__988922976676775__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/4nwx/A/4nwx_A.pdb.gz

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/4nwx/A/4nwx_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/4nwx/A/4nwx_A.pdb.gz): 222 ms

reading 503 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

503 atoms created

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

Time for creating model: 31 ms

Adding embedded #jmolscript: select ({0:502});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

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

Viewer cachePut cache://localLOAD_/static/knot_data/4nwx/A/4nwx_A.pdb.gz

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

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	6-443	438	1-5	453-503	444-452	5	51	slipknot

sequence length	503
structure length	503
publication title	Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism pubmed doi rcsb
molecule tags	Isomerase
molecule keywords	2,3-bisphosphoglycerate-independent phosphoglycerate mutase
source organism	Staphylococcus aureus subsp. aureus
total genus	Genus: 194
ec nomenclature	ec 5.4.2.12: Phosphoglycerate mutase (2,3-diphosphoglycerate-independent).
pdb deposition date	2013-12-07
KnotProt deposition date	2015-02-11

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01676	Metalloenzyme	Metalloenzyme superfamily

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

1EJJA 1EQJA 1O98A 1O99A 2IFYA 4NWJA 4NWXA 4QAXA
similar chains in the KnotProt database (40% sequence similarity)

7TL8A
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
1EJJ A; 1EQJ A; 1O98 A; 1O99 A; 2IFY A; 4NWJ A; 4NWX A; 4QAX A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
7TL8 A;

4NWXA

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁