6NJ6 | KnotProt

6NJ6A

Thermostable variant of human carbonic anhydrase with tetrazine 2.0 at site 186 reacted with stco in crystallo

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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 75

Slipknot S +3₁

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setting document base to "https://knotprot.cent.uw.edu.pl/view/6nj6/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

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__779753045417656__ 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	26-254	229	1-25, 255-259			25	5	knot

Chain Sequence

HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHTFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSHDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSANPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLP-SLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVSKFRKLNFNGEGEPEEPMVDNWRPTQPLKNRQIKASFKH

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

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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__779753045417656__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__779753045417656__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/6nj6/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

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__779753045417656__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/6nj6/A/6nj6_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/6nj6/A/6nj6_A.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/6nj6/A/6nj6_A.pdb.gz

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/6nj6/A/6nj6_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/6nj6/A/6nj6_A.pdb.gz): 294 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: 35 ms

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

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Script completed

Jmol script terminated

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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/6nj6/A/6nj6_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/6nj6/A/6nj6_A.pdb.gz): 23 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: 36 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

Viewer cachePut cache://localLOAD_/static/knot_data/6nj6/A/6nj6_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/6nj6/A/6nj6_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/6nj6/A/6nj6_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/6nj6/A/6nj6_A.pdb.gz): 26 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: 29 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/6nj6/A/6nj6_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/6nj6/A/6nj6_A.pdb.gz): 13 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: 30 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	24-254	231	1-23, 255-259	23	5	knot
view details	+ 3₁	24-233	210	1-23, 234-238	23	5	knot
view details	+ 3₁	26-231	206	1-25, 232-236	25	4	slipknot

	Fingerprint	Knot forming loop	Loop type
knots details	K +3₁	His3 ... His93 <-> Bridging ionZn306 <-> His95 ... Chain closureHis261 <-> His3	probabilistic	color sequence
knots details	K +3₁	Chain closureHis3 <-> His261 ... His118 <-> Bridging ionZn306 <-> His95 ... His3	probabilistic	color sequence
knots details	K +3₁	His3 ... His93 <-> Bridging ionZn306 <-> His118 ... Chain closureHis261 <-> 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

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Jmol JavaScript applet jmolApplet2__779753045417656__ initializing

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AppletRegistry.checkIn(jmolApplet2__779753045417656__)

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setting document base to "https://knotprot.cent.uw.edu.pl/view/6nj6/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__779753045417656__ 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	26-255	230	1-25, 256-258			25	3	knot
view details				2.1	24-251	228	1-23	256-258	252-255	23	3	slipknot

sequence length	258
structure length	257
publication title	Immobilization of Proteins with Controlled Load and Orientation. pubmed doi rcsb
molecule tags	Lyase
molecule keywords	Carbonic anhydrase 2
source organism	Homo sapiens
missing residues	183
total genus	Genus: 75
ec nomenclature	ec 4.2.1.1: Alcohol dehydrogenase.
pdb deposition date	2019-01-02
KnotProt deposition date	2019-10-17

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)

6B00A 6NJ3A 6NJ4A 6NJ5A 6NJ6A
similar chains in the KnotProt database (40% sequence similarity)

9F2EA 9F2FA 9JWEA 9JWUA
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
6B00 A; 6NJ3 A; 6NJ4 A; 6NJ5 A; 6NJ6 A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
9F2E A; 9F2F A; 9JWE A; 9JWU A;

How to cite

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling

Application loaded.

6NJ6A

Slipknot S +31

Chain Sequence

Knot K 3x +31

Chain Sequence

pfam database annotations

Slipknot S +3₁

Knot K 3x +3₁