5G01 | KnotProt

Genus: 80
Alphaknot: P00918

Knot K +3₁

script 1 started

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JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__0680316252225195__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__0680316252225195__)

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setting document base to "https://knotprot.cent.uw.edu.pl/view/5G01/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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memory: 0.0/0.0

processors available: 1

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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__0680316252225195__ 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, 256-259			21	4	knot

Chain Sequence

HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFKVNFDDSQDKAVLKGGPLDGTYRLTQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDASKASQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLNETVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK

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__0680316252225195__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__0680316252225195__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/5G01/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__0680316252225195__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"0680316252225195","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/5G01/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__0680316252225195__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/5g01/A/5g01_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5g01/A/5g01_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5g01/A/5g01_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/5g01/A/5g01_A.pdb.gz): 870 ms

reading 258 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

258 atoms created

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

Time for creating model: 43 ms

Adding embedded #jmolscript: select ({0:257});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

Viewer cachePut cache://localLOAD_/static/knot_data/5g01/A/5g01_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5g01/A/5g01_A.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/5g01/A/5g01_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5g01/A/5g01_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5g01/A/5g01_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/5g01/A/5g01_A.pdb.gz): 22 ms

reading 258 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

258 atoms created

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

Time for creating model: 30 ms

Adding embedded #jmolscript: select ({0:257});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/5g01/A/5g01_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/5g01/A/5g01_A.pdb.gz): 18 ms

reading 258 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

258 atoms created

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

Time for creating model: 16 ms

Adding embedded #jmolscript: select ({0:257});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5g01/A/5g01_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/5g01/A/5g01_A.pdb.gz): 30 ms

reading 258 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

258 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:257});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	21-255	235	1-20, 256-259	20	4	knot
view details	+ 3₁	25-234	210	1-24, 235-238	24	4	knot
view details	+ 3₁	24-233	210	1-23, 234-236	23	3	knot

	Fingerprint	Knot forming loop	Loop type
knots details	K +3₁	Chain closureHis3 <-> Lys261 ... His96 <-> Bridging ionZn1262 <-> His94 ... His3	probabilistic	color sequence
knots details	K +3₁	His3 ... His96 <-> Bridging ionZn1262 <-> His119 ... Chain closureLys261 <-> His3	probabilistic	color sequence
knots details	K +3₁	His3 ... His94 <-> Bridging ionZn1262 <-> His119 ... Chain closureLys261 <-> His3	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__0680316252225195__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet2__0680316252225195__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/5G01/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__0680316252225195__ 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				3.1	25-257	233	1-24, 258-258			24	1	knot
view details				2.1	25-252	228	1-24	258-258	253-257	24	1	slipknot

sequence length	258
structure length	258
publication title	An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structures of Psammaplin C. pubmed doi rcsb
molecule tags	Lyase
molecule keywords	CARBONIC ANHYDRASE 2
source organism	Homo sapiens
total genus	Genus: 80
ec nomenclature
pdb deposition date	2016-03-16
KnotProt deposition date	2018-10-20

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

4Q08A 4Q09A 5G0CA 6YH4A 6YH5A
similar chains in the KnotProt database (40% sequence similarity)

8QHJA 8QUFAAA 8RLQAAA 8RNSA
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
4Q08 A; 4Q09 A; 5G0C A; 
#similar chains, but unknotted
6YH5 A; 
#similar chains in the pdb database (40% sequence similarity)
8QHJ A; 8QUF AAA; 8RLQ AAA; 8RNS A;

5G01A

Knot K +31

Chain Sequence

Knot K 3x +31

Chain Sequence

Knot K +3₁

Knot K 3x +3₁