4YWP | KnotProt

Genus: 72
Alphaknot: P00918

Knot K +3₁

script 1 started

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JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__8792225523571782__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__8792225523571782__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/4ywp/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:jmolApplet1 (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 jmolApplet1__8792225523571782__ 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	22-255	234	1-21, 256-258			21	3	knot

Chain Sequence

HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK

Note, that the numbers in the matrix denote the consecutive residues in the loop, not the index of amino acids in the chain!

Knot K 3x +3₁

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__8792225523571782__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8792225523571782__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/4ywp/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__8792225523571782__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8792225523571782","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/4ywp/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__8792225523571782__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/4ywp/A/4ywp_A.pdb.gz

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

Viewer cachePut cache://localLOAD_/static/knot_data/4ywp/A/4ywp_A.pdb.gz

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

Viewer cachePut cache://localLOAD_/static/knot_data/4ywp/A/4ywp_A.pdb.gz

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/4ywp/A/4ywp_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/4ywp/A/4ywp_A.pdb.gz): 512 ms

reading 257 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

257 atoms created

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

Time for creating model: 73 ms

Adding embedded #jmolscript: select ({0:256});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

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

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/4ywp/A/4ywp_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/4ywp/A/4ywp_A.pdb.gz): 22 ms

reading 257 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

257 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:256});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(/static/knot_data/4ywp/A/4ywp_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/4ywp/A/4ywp_A.pdb.gz): 25 ms

reading 257 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

257 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:256});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

FileManager.getAtomSetCollectionFromFile(/static/knot_data/4ywp/A/4ywp_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/4ywp/A/4ywp_A.pdb.gz): 31 ms

reading 257 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

257 atoms created

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

Time for creating model: 12 ms

Adding embedded #jmolscript: select ({0:256});backbone only;select *;

platformSpeed = 6

specularPower = 1

ambientPercent = 20

Script completed

Jmol script terminated

Help Knotting data interpretation Full screen

		Knot core range	Knot core length	Knot tails range	N-end length	C-end length	Type
view details	+ 3₁	19-255	237	1-18, 256-258	18	3	knot
view details	+ 3₁	24-234	211	1-23, 235-237	23	3	knot
view details	+ 3₁	22-233	212	1-21, 234-235	21	2	knot

	Fingerprint	Knot forming loop	Loop type
knots details	K +3₁	His4 ... His94 <-> Bridging ionZn301 <-> His96 ... Chain closureLys261 <-> His4	probabilistic	color sequence
knots details	K +3₁	His4 ... His96 <-> Bridging ionZn301 <-> His119 ... Chain closureLys261 <-> His4	probabilistic	color sequence
knots details	K +3₁	His4 ... His94 <-> Bridging ionZn301 <-> His119 ... Chain closureLys261 <-> His4	probabilistic	color sequence

Chain Sequence

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

script 1 started

platformSpeed = 8

JSmol exec jmolApplet2 start applet null

Jmol JavaScript applet jmolApplet2__8792225523571782__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet2__8792225523571782__)

vwrOptions:

{ "name":"jmolApplet2","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/4ywp/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet2__8792225523571782__","codePath":"https:/static/js/j2s/","display":"jmolApplet2_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8792225523571782","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/4ywp/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:jmolApplet2 (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 jmolApplet2__8792225523571782__ ready

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	25-251	227	1-24	257-257	252-256	24	1	slipknot

sequence length	257
structure length	257
publication title	A sucrose-binding site provides a lead towards an isoform-specific inhibitor of the cancer-associated enzyme carbonic anhydrase IX. pubmed doi rcsb
molecule tags	Lyase
molecule keywords	Carbonic anhydrase 2
source organism	Homo sapiens
total genus	Genus: 72
ec nomenclature	ec 4.2.1.1: Carbonic anhydrase.
pdb deposition date	2015-03-20
KnotProt deposition date	2018-10-20

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00194	Carb_anhydrase	Eukaryotic-type carbonic anhydrase

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

4R59A 4R5AA 4RIUA 4RIVA 4YWPA 4ZAOA 4ZWXA 4ZWZA 5JMZA
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)
4R59 A; 4R5A A; 4RIU A; 4RIV A; 4YWP A; 4ZAO A; 4ZWX A; 4ZWZ A; 5JMZ A; 
#similar chains, but unknotted

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

4YWPA

Knot K +31

Chain Sequence

Knot K 3x +31

Chain Sequence

pfam database annotations

Knot K +3₁

Knot K 3x +3₁