1P75 | KnotProt

Genus: 112

Slipknot S +3₁

script 1 started

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setting document base to "https://knotprot.cent.uw.edu.pl/view/1p75/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

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language=en_US

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Jmol applet jmolApplet1__119295442785067__ 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	6-116	111	1-5	309-332	117-308	5	24	slipknot

Chain Sequence

HMVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRAR-GEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMGV

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__119295442785067__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__119295442785067__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/1p75/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__119295442785067__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"119295442785067","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/1p75/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

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Jmol getValue SYNCCallback null

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language=en_US

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Jmol applet jmolApplet0__119295442785067__ ready

script 1 started

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Viewer cachePut cache://localLOAD_/static/knot_data/1p75/A/1p75_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1p75/A/1p75_A.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/1p75/A/1p75_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1p75/A/1p75_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1p75/A/1p75_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/1p75/A/1p75_A.pdb.gz): 824 ms

reading 331 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

331 atoms created

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

Time for creating model: 55 ms

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Script completed

Jmol script terminated

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loadScript /static/js/j2s/J/shape/Mesh.js

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1p75/A/1p75_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/1p75/A/1p75_A.pdb.gz): 38 ms

reading 331 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

331 atoms created

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

Time for creating model: 45 ms

Adding embedded #jmolscript: select ({0:330});backbone only;select *;

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cartoonsFancy = true

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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	6-160	155	1-5	296-331	161-295	5	36	slipknot
view details	2.1	9-120	112		1-2, 162-331	3-8, 121-161	2	170	slipknot
view details	3.1	9-162	154		1-5, 180-331	6-8, 163-179	5	152	slipknot
view details	2.1	9-179	171		1-5, 181-331	6-8, 180-180	5	151	slipknot
view details	2.1	9-180	172		1-5, 279-331	6-8, 181-278	5	53	slipknot
view details	3.1	9-284	276		1-2, 307-331	3-8, 285-306	2	25	slipknot
view details	2.1	9-278	270		1-5, 285-331	6-8, 279-284	5	47	slipknot

sequence length	332
structure length	331
publication title	Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases. pubmed doi rcsb
molecule tags	Transferase
molecule keywords	Thymidine kinase
source organism	Equid herpesvirus 4
missing residues	179
total genus	Genus: 112
ec nomenclature	ec 2.7.1.21: Thymidine kinase.
pdb deposition date	2003-04-30
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00693	Herpes_TK	Thymidine kinase from herpesvirus

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	1p75A00

1II9A 1KI6A 1KI7A 3VTKA 1KI8A 2VTKA 1GKUB 1KI4A 1P73A 1E2NA 1P72A 1KI6B 3RDPA 1E2LA 1E2IA 1OSNA 3F0TA 4IVPA 1E2JA 1E2HA 1KI2A 1KIMA 1E2KA 1OF1A 4IVQA 4JBXA 4JBYA 1QHIA 1P6XA 1KI3A 2KI5A 1P75A 1E2MA 4IVRA 1F48A 1VTKA 1P7CA 1E2PA
chains in the KnotProt database with same CATH superfamily

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

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

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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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1P75A

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁