3TG0 | KnotProt

Genus: 164

Slipknot S +3₁

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setting document base to "https://knotprot.cent.uw.edu.pl/view/3TG0/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

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java.version: 2018-01-28 23:38:52 (JSmol/j2s)

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Jmol getValue emulate null

defaults = "Jmol"

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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__8174623921452304__ 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	38-359	322	1-37	411-440	360-410	37	30	slipknot

Chain Sequence

NRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGL

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__8174623921452304__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8174623921452304__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/3TG0/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

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Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

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Viewer cachePut cache://localLOAD_/static/knot_data/3tg0/A/3tg0_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3tg0/A/3tg0_A.pdb.gz

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Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3tg0/A/3tg0_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3tg0/A/3tg0_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/3tg0/A/3tg0_A.pdb.gz): 1148 ms

reading 440 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

440 atoms created

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

Time for creating model: 43 ms

Adding embedded #jmolscript: select ({0:439});backbone only;select *;

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3tg0/A/3tg0_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/3tg0/A/3tg0_A.pdb.gz): 18 ms

reading 440 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

440 atoms created

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

Time for creating model: 16 ms

Adding embedded #jmolscript: select ({0:439});backbone only;select *;

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Jmol script terminated

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

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	2.1	37-359	323	1-36	367-440	360-366	36	74	slipknot
view details	3.1	40-363	324	1-39	406-440	364-405	39	35	slipknot
view details	3.1	40-405	366	1-39	408-440	406-407	39	33	slipknot
view details	2.1	36-407	372	1-35	413-440	408-412	35	28	slipknot

sequence length	440
structure length	440
publication title	High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography. pubmed doi rcsb
molecule tags	Hydrolase
molecule keywords	Alkaline phosphatase
source organism	Escherichia coli
total genus	Genus: 164
ec nomenclature	ec 3.1.3.1: Alkaline phosphatase.
pdb deposition date	2011-08-16
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00245	Alk_phosphatase	Alkaline phosphatase

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

1ED8A 1ED9A 1EW8A 1EW9A 1Y6VA 3BDGB 3BDHA 3TG0A 5C66A
similar chains in the KnotProt database (40% sequence similarity)

None
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
1ED8 A; 1ED9 A; 1EW8 A; 1EW9 A; 1Y6V A; 3BDG B; 3BDH A; 3TG0 A; 5C66 A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)

3TG0A

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁