1YH1 | KnotProt

Knot K +3₁

script 1 started

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JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__8819875297985567__ initializing

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AppletRegistry.checkIn(jmolApplet1__8819875297985567__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/1yh1/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

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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__8819875297985567__ 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	174-251	78	1-173, 252-334			173	83	knot

Chain Sequence

LKHFLNTQDWSRAELDALLTQAALFKRNKLGSELKGKSIALVFFNPSMRTRTSFELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVDWSKDREDQVLKSFAKYSPVPVINMETITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALVGQ

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__8819875297985567__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8819875297985567__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/1yh1/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__8819875297985567__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8819875297985567","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/1yh1/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__8819875297985567__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/1yh1/A/1yh1_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1yh1/A/1yh1_A.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/1yh1/A/1yh1_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1yh1/A/1yh1_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1yh1/A/1yh1_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/1yh1/A/1yh1_A.pdb.gz): 484 ms

reading 334 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

334 atoms created

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

Time for creating model: 59 ms

Adding embedded #jmolscript: select ({0:333});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/1yh1/A/1yh1_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/1yh1/A/1yh1_A.pdb.gz): 15 ms

reading 334 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

334 atoms created

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

Time for creating model: 24 ms

Adding embedded #jmolscript: select ({0:333});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

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	3.1	174-251	78	1-173, 252-334			173	83	knot
view details	2.1	133-248	116		1-4, 252-334	5-132, 249-251	4	83	slipknot
view details	2.1	155-249	95		1-133, 252-334	134-154, 250-251	133	83	slipknot
view details	3.1	175-284	110		1-173, 291-334	174-174, 285-290	173	44	slipknot
view details	2.1	175-322	148	323-334	1-173	174-174	173	11	slipknot

sequence length	334
structure length	334
publication title	Crystal structure of N-acetylornithine transcarbamylase from Xanthomonas campestris: a novel enzyme in a new arginine biosynthetic pathway found in several eubacteria. pubmed doi rcsb
molecule tags	Hydrolase
molecule keywords	N-acetyl-L-ornithine carbamoyltransferase
source organism	Xanthomonas campestris
ec nomenclature
pdb deposition date	2005-01-06
KnotProt deposition date	2014-07-31

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.50.1370	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rossmann fold	1yh1A01
3.40.50.1370	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rossmann fold	1yh1A02

3KZOA 2FG6C 3M5DA 3KZMA 3M5CA 3M4NA 3L06A 1JS1X 3KZNA 3L04A 2G7MC 3KZKA 1YH1A 3L05A 3KZCA 3M4JA 3L02A
chains in the KnotProt database with same CATH superfamily

1YVEI 3F0TA 1E2MA 1KI7A 1OF1A 3M5DA 2KI5A 3M5CA 3M4NA 3KZMA 1E2KA 1JS1X 1P72A 1R4NB 1R4MB 2G7MC 3FSGA 4JBXA 1QMGA 3KZOA 4IVRA 1F48A 1KI8A 1E2NA 1KI6B 1KI4A 3L06A 2VTKA 1E2IA 1KI2A 1KIMA 1E2PA 3KZCA 1KI6A 2FG6C 1E2JA 4IVPA 4IVQA 1KI3A 1LNSA 1P73A 1DBIA 1E2LA 1E2HA 3RDPA 1VTKA 1P6XA 1OSNA 1YH1A 3L05A 3FR8A 1P7CA 3L02A 3M4JA 2XTJA 1P75A 1II9A 3VTKA 3KZNA 3L04A 1YRLA 3KZKA 4JBYA 1GKUB 3FR7A 1QHIA
chains in the KnotProt database with same CATH topology

3M5DA 3KZMA 3M5CA 3M4NA 1JS1X 2G7MC 3FSGA 3KZOA 3L06A 3KZCA 2FG6C 1LNSA 1DBIA 1YH1A 3L05A 3M4JA 3L02A 2XTJA 3KZNA 3L04A 3KZKA 1GKUB
chains in the KnotProt database with same CATH homology

#chains in the KnotProt database with same CATH superfamily
 3KZO A;  2FG6 C;  3M5D A;  3KZM A;  3M5C A;  3M4N A;  3L06 A;  1JS1 X;  3KZN A;  3L04 A;  2G7M C;  3KZK A;  1YH1 A;  3L05 A;  3KZC A;  3M4J A;  3L02 A; 
#chains in the KnotProt database with same CATH topology
 1YVE I;  3F0T A;  1E2M A;  1KI7 A;  1OF1 A;  3M5D A;  2KI5 A;  3M5C A;  3M4N A;  3KZM A;  1E2K A;  1JS1 X;  1P72 A;  1R4N B;  1R4M B;  2G7M C;  3FSG A;  4JBX A;  1QMG A;  3KZO A;  4IVR A;  1F48 A;  1KI8 A;  1E2N A;  1KI6 B;  1KI4 A;  3L06 A;  2VTK A;  1E2I A;  1KI2 A;  1KIM A;  1E2P A;  3KZC A;  1KI6 A;  2FG6 C;  1E2J A;  4IVP A;  4IVQ A;  1KI3 A;  1LNS A;  1P73 A;  1DBI A;  1E2L A;  1E2H A;  3RDP A;  1VTK A;  1P6X A;  1OSN A;  1YH1 A;  3L05 A;  3FR8 A;  1P7C A;  3L02 A;  3M4J A;  2XTJ A;  1P75 A;  1II9 A;  3VTK A;  3KZN A;  3L04 A;  1YRL A;  3KZK A;  4JBY A;  1GKU B;  3FR7 A;  1QHI A; 
#chains in the KnotProt database with same CATH homology
 3M5D A;  3KZM A;  3M5C A;  3M4N A;  1JS1 X;  2G7M C;  3FSG A;  3KZO A;  3L06 A;  3KZC A;  2FG6 C;  1LNS A;  1DBI A;  1YH1 A;  3L05 A;  3M4J A;  3L02 A;  2XTJ A;  3KZN A;  3L04 A;  3KZK A;  1GKU B;

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similar chains in the KnotProt database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the KnotProt database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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1YH1A

Knot K +31

Chain Sequence

Knot K +3₁