1KH7 | KnotProt

Genus: 151

Slipknot S +3₁

script 1 started

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setting document base to "https://knotprot.cent.uw.edu.pl/view/1KH7/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)

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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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Jmol applet jmolApplet1__8135059504302733__ 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	41-363	323	1-40	414-444	364-413	40	31	slipknot

Chain Sequence

VLENRAAQGNITAPGGARRLTGDQTAALRNSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQGATPAALVAHVTSRKCYGPSKTSQKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREEAEARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQNHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK

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__8135059504302733__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8135059504302733__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/1KH7/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 IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

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Jmol applet jmolApplet0__8135059504302733__ ready

script 1 started

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Viewer cachePut cache://localLOAD_/static/knot_data/1kh7/A/1kh7_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1kh7/A/1kh7_A.pdb.gz

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Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1kh7/A/1kh7_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1kh7/A/1kh7_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/1kh7/A/1kh7_A.pdb.gz): 616 ms

reading 444 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

444 atoms created

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

Time for creating model: 47 ms

Adding embedded #jmolscript: select ({0:443});backbone only;select *;

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Script completed

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loadScript /static/js/j2s/J/renderbio/BioMeshRenderer.js

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1kh7/A/1kh7_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/1kh7/A/1kh7_A.pdb.gz): 25 ms

reading 444 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

444 atoms created

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

Time for creating model: 31 ms

Adding embedded #jmolscript: select ({0:443});backbone only;select *;

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cartoonsFancy = true

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traceAlpha = true

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Script completed

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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	39-362	324	1-38	370-444	363-369	38	75	slipknot
view details	3.1	44-365	322	1-43	383-444	366-382	43	62	slipknot
view details	3.1	44-382	339	1-43	407-444	383-406	43	38	slipknot
view details	3.1	44-406	363	1-43	412-444	407-411	43	33	slipknot
view details	2.1	39-411	373	1-38	416-444	412-415	38	29	slipknot
view details	2.1	40-411	372		1-38, 414-444	39-39, 412-413	38	31	slipknot

sequence length	444
structure length	444
publication title	Artificial evolution of an enzyme active site: structural studies of three highly active mutants of Escherichia coli alkaline phosphatase. pubmed doi rcsb
molecule tags	Hydrolase
molecule keywords	alkaline phosphatase
source organism	Escherichia coli
total genus	Genus: 151
ec nomenclature	ec 3.1.3.1: Alkaline phosphatase.
pdb deposition date	2001-11-29
KnotProt deposition date	2014-07-31

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	1kh7A00

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;

1AJAA 1ALKA 1KH4A 1KH5A 1KH9A 1KHJA 1KHKA 1KHLA 1KHNA
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)
1AJA A; 1ALK A; 1KH4 A; 1KH5 A; 1KH9 A; 1KHJ A; 1KHK A; 1KHL A; 1KHN A; 
#similar chains, but unknotted

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

1KH7A

Slipknot S +31

Chain Sequence

Slipknot S +3₁