3L06 | KnotProt

Genus: 120

Knot K +3₁

script 1 started

platformSpeed = 8

JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__528031373491209__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__528031373491209__)

vwrOptions:

{ "name":"jmolApplet1","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/3L06/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__528031373491209__","codePath":"https:/static/js/j2s/","display":"jmolApplet1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"528031373491209","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/3L06/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__528031373491209__ 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, 252-332			173	81	knot

Chain Sequence

LKHFLNTQDWSRAELDALLTQAALFKRNKLGSELKGKSIALVFFNPSMRTRTSFELGAFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTVEHIAEVARVLGRYVDLIGVRAFPKFVDWSKDREDQVLKSFAKYSPVPVINMETITHPCQELAHALALQEHFGTPDLRGKKYVLTWTYHPKPLNTAVANSALTIATRMGMDVTLLCPTPDYILDERYMDWAAQNVAESGGSLQVSHDIDSAYAGADVVYAKSWGALPFFGNWEPEKPIRDQYQHFIVDERKMALTNNGVFSHCLPLRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAALV

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__528031373491209__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__528031373491209__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/3L06/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__528031373491209__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"528031373491209","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/3L06/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__528031373491209__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/3l06/A/3l06_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3l06/A/3l06_A.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/3l06/A/3l06_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3l06/A/3l06_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3l06/A/3l06_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/3l06/A/3l06_A.pdb.gz): 678 ms

reading 332 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

332 atoms created

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

Time for creating model: 36 ms

Adding embedded #jmolscript: select ({0:331});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/3l06/A/3l06_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/3l06/A/3l06_A.pdb.gz): 14 ms

reading 332 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

332 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:331});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	173-251	79	1-172, 252-332			172	81	knot
view details	3.1	174-253	80	254-332	1-172	173-173	172	78	slipknot
view details	2.1	170-248	79		1-32, 252-332	33-169, 249-251	32	81	slipknot
view details	2.1	175-280	106		1-173, 286-332	174-174, 281-285	173	47	slipknot
view details	2.1	175-286	112		1-173, 290-332	174-174, 287-289	173	43	slipknot
view details	2.1	175-297	123		1-173, 304-332	174-174, 298-303	173	29	slipknot

sequence length	332
structure length	332
publication title	A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase. pubmed doi rcsb
molecule tags	Transferase
molecule keywords	N-acetylornithine carbamoyltransferase
source organism	Xanthomonas campestris pv. campestris
total genus	Genus: 120
ec nomenclature	ec 2.1.3.9: N-acetylornithine carbamoyltransferase.
pdb deposition date	2009-12-09
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00185	OTCace	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain

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	3l06A01
3.40.50.1370	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rossmann fold	3l06A02

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;

...loading similar chains, please wait...
similar chains in the KnotProt database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the KnotProt database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

3L06A

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁