1ALI | KnotProt

Genus: 162

Slipknot S +3₁

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setting document base to "https://knotprot.cent.uw.edu.pl/view/1ali/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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APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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language=en_US

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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	43-366	324	1-42	416-446	367-415	42	31	slipknot

Chain Sequence

MPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQENTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK

Whole chain analysis

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Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__932864243878857__ initializing

Jmol getValue debug null

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AppletRegistry.checkIn(jmolApplet0__932864243878857__)

vwrOptions:

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

Jmol getValue MEASURECallback null

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Jmol applet jmolApplet0__932864243878857__ ready

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platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/1ali/A/1ali_A.pdb.gz

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

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1ali/A/1ali_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/1ali/A/1ali_A.pdb.gz): 788 ms

reading 446 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

446 atoms created

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

Time for creating model: 50 ms

Adding embedded #jmolscript: select ({0:445});backbone only;select *;

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1ali/A/1ali_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/1ali/A/1ali_A.pdb.gz): 18 ms

reading 446 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

446 atoms created

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

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:445});backbone only;select *;

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cartoonsFancy = true

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traceAlpha = true

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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	44-370	327	1-43	414-446	371-413	43	33	slipknot
view details	3.1	42-413	372	1-41	418-446	414-417	41	29	slipknot
view details	2.1	13-364	352		1-2, 369-446	3-12, 365-368	2	78	slipknot
view details	2.1	37-363	327		1-6, 370-446	7-36, 364-369	6	77	slipknot
view details	2.1	37-369	333		1-6, 371-446	7-36, 370-370	6	76	slipknot
view details	2.1	42-365	324		1-38, 370-446	39-41, 366-369	38	77	slipknot

sequence length	446
structure length	446
publication title	Escherichia coli alkaline phosphatase: X-ray structural studies of a mutant enzyme (His-412-->Asn) at one of the catalytically important zinc binding sites. pubmed rcsb
molecule tags	Hydrolase (phosphoric monoester)
molecule keywords	ALKALINE PHOSPHATASE
source organism	Escherichia coli
total genus	Genus: 162
ec nomenclature	ec 3.1.3.1: Alkaline phosphatase.
pdb deposition date	1995-06-02
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)

cath code	Class	Architecture	Topology	Homology	Domain
3.40.720.10	Alpha Beta	3-Layer(aba) Sandwich	Alkaline Phosphatase, subunit A	Alkaline Phosphatase, subunit A	1aliA00

1ZEBA 1AJAA 1ALJA 2GLQA 3TWZA 1KH4A 1KH7A 1ANJA 2GA3A 1KHKA 3NVLA 3UN5A 3M7VA 1N2KA 1ELYA 1AUKA 1E1ZP 1O99A 3OT9A 1KH5A 3M8ZA 1HDHA 1URBA 3SZZA 1K7HA 1ELZA 2QZUA 1EI6A 1HJKA 1KHLA 1FSUA 3T01A 1E2SP 1ZEDA 1AJCA 1SHQA 3CMRA 1EQJA 1EW2A 3UN3A 3IGZB 1B8JA 2IFYA 3SZYA 1ED8A 1ANIA 2ANHA 1ZEFA 3UO0A 1KH9A 3TX0A 3MK2A 4FDIA 3M8YA 1ALIA 4FDJA 1E3CP 1EW9A 3UNYA 2G9YA 1ALKA 3ED4A 3DPCA 1ELXA 1EW8A 1O98A 1AJDA 1AJBA 3T02A 3T00A 1N2LA 3MK0A 1EJJA 1Y6VA 3BDFA 1URAA 1KHNA 1Y7AA 3M8WA 3MK1A 3UN2A 1E33P 1P49A 3DYCA 1HQAA 1ED9A 1SHNA 3BDGA 3BDHA 3IGYB 1KHJA 3BDGB
chains in the KnotProt database with same CATH superfamily

#chains in the KnotProt database with same CATH superfamily
 1ZEB A;  1AJA A;  1ALJ A;  2GLQ A;  3TWZ A;  1KH4 A;  1KH7 A;  1ANJ A;  2GA3 A;  1KHK A;  3NVL A;  3UN5 A;  3M7V A;  1N2K A;  1ELY A;  1AUK A;  1E1Z P;  1O99 A;  3OT9 A;  1KH5 A;  3M8Z A;  1HDH A;  1URB A;  3SZZ A;  1K7H A;  1ELZ A;  2QZU A;  1EI6 A;  1HJK A;  1KHL A;  1FSU A;  3T01 A;  1E2S P;  1ZED A;  1AJC A;  1SHQ A;  3CMR A;  1EQJ A;  1EW2 A;  3UN3 A;  3IGZ B;  1B8J A;  2IFY A;  3SZY A;  1ED8 A;  1ANI A;  2ANH A;  1ZEF A;  3UO0 A;  1KH9 A;  3TX0 A;  3MK2 A;  4FDI A;  3M8Y A;  1ALI A;  4FDJ A;  1E3C P;  1EW9 A;  3UNY A;  2G9Y A;  1ALK A;  3ED4 A;  3DPC A;  1ELX A;  1EW8 A;  1O98 A;  1AJD A;  1AJB A;  3T02 A;  3T00 A;  1N2L A;  3MK0 A;  1EJJ A;  1Y6V A;  3BDF A;  1URA A;  1KHN A;  1Y7A A;  3M8W A;  3MK1 A;  3UN2 A;  1E33 P;  1P49 A;  3DYC A;  1HQA A;  1ED9 A;  1SHN A;  3BDG A;  3BDH A;  3IGY B;  1KHJ A;  3BDG B; 
#chains in the KnotProt database with same CATH topology
 1ZEB A;  1AJA A;  1ALJ A;  2GLQ A;  3TWZ A;  1KH4 A;  1KH7 A;  1ANJ A;  2GA3 A;  1KHK A;  3NVL A;  3UN5 A;  3M7V A;  1N2K A;  1ELY A;  1AUK A;  1E1Z P;  1O99 A;  3OT9 A;  1KH5 A;  3M8Z A;  1HDH A;  1URB A;  3SZZ A;  1K7H A;  1ELZ A;  2QZU A;  1EI6 A;  1HJK A;  1KHL A;  1FSU A;  3T01 A;  1E2S P;  1ZED A;  1AJC A;  1SHQ A;  3CMR A;  1EQJ A;  1EW2 A;  3UN3 A;  3IGZ B;  1B8J A;  2IFY A;  3SZY A;  1ED8 A;  1ANI A;  2ANH A;  1ZEF A;  3UO0 A;  1KH9 A;  3TX0 A;  3MK2 A;  4FDI A;  3M8Y A;  1ALI A;  4FDJ A;  1E3C P;  1EW9 A;  3UNY A;  2G9Y A;  1ALK A;  3ED4 A;  3DPC A;  1ELX A;  1EW8 A;  1O98 A;  1AJD A;  1AJB A;  3T02 A;  3T00 A;  1N2L A;  3MK0 A;  1EJJ A;  1Y6V A;  3BDF A;  1URA A;  1KHN A;  1Y7A A;  3M8W A;  3MK1 A;  3UN2 A;  1E33 P;  1P49 A;  3DYC A;  1HQA A;  1ED9 A;  1SHN A;  3BDG A;  3BDH A;  3IGY B;  1KHJ A;  3BDG B; 
#chains in the KnotProt database with same CATH homology
 1ZEB A;  1AJA A;  1ALJ A;  2GLQ A;  3TWZ A;  1KH4 A;  1KH7 A;  1ANJ A;  2GA3 A;  1KHK A;  3NVL A;  3UN5 A;  3M7V A;  1N2K A;  1ELY A;  1AUK A;  1E1Z P;  1O99 A;  3OT9 A;  1KH5 A;  3M8Z A;  1HDH A;  1URB A;  3SZZ A;  1K7H A;  1ELZ A;  2QZU A;  1EI6 A;  1HJK A;  1KHL A;  1FSU A;  3T01 A;  1E2S P;  1ZED A;  1AJC A;  1SHQ A;  3CMR A;  1EQJ A;  1EW2 A;  3UN3 A;  3IGZ B;  1B8J A;  2IFY A;  3SZY A;  1ED8 A;  1ANI A;  2ANH A;  1ZEF A;  3UO0 A;  1KH9 A;  3TX0 A;  3MK2 A;  4FDI A;  3M8Y A;  1ALI A;  4FDJ A;  1E3C P;  1EW9 A;  3UNY A;  2G9Y A;  1ALK A;  3ED4 A;  3DPC A;  1ELX A;  1EW8 A;  1O98 A;  1AJD A;  1AJB A;  3T02 A;  3T00 A;  1N2L A;  3MK0 A;  1EJJ A;  1Y6V A;  3BDF A;  1URA A;  1KHN A;  1Y7A A;  3M8W A;  3MK1 A;  3UN2 A;  1E33 P;  1P49 A;  3DYC A;  1HQA A;  1ED9 A;  1SHN A;  3BDG A;  3BDH A;  3IGY B;  1KHJ A;  3BDG B;

1ALJA 1B8JA 1ED8A 1ED9A 1EW8A 1EW9A 1HQAA 1Y6VA 3BDGB
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)
1ALJ A; 1B8J A; 1ED8 A; 1ED9 A; 1EW8 A; 1EW9 A; 1HQA A; 1Y6V A; 3BDG B; 
#similar chains, but unknotted

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

1ALIA

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁