3KBC | KnotProt

Genus: 139

Slipknot S +3₁

script 1 started

platformSpeed = 8

JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__934290427839259__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__934290427839259__)

vwrOptions:

{ "name":"jmolApplet1","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/3kbc/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__934290427839259__","codePath":"https:/static/js/j2s/","display":"jmolApplet1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"934290427839259","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/3kbc/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__934290427839259__ 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	46-321	276	1-45	339-411	322-338	45	73	slipknot

Chain Sequence

KYIEYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLCMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLCMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE

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__934290427839259__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__934290427839259__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/3kbc/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__934290427839259__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"934290427839259","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/3kbc/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__934290427839259__ ready

script 1 started

platformSpeed = 8

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	47-312	266	1-46	346-411	313-345	46	66	slipknot
view details	2.1	40-358	319	1-39	368-411	359-367	39	44	slipknot
view details	2.1	61-316	256		1-47, 328-411	48-60, 317-327	47	84	slipknot
view details	2.1	60-331	272		1-52, 344-411	53-59, 332-343	52	68	slipknot

sequence length	411
structure length	411
publication title	Transport mechanism of a bacterial homologue of glutamate transporters. pubmed doi rcsb
molecule tags	Transport protein
molecule keywords	425aa long hypothetical proton glutamate symport protein
source organism	Pyrococcus horikoshii
total genus	Genus: 139
ec nomenclature
pdb deposition date	2009-10-20
KnotProt deposition date	2014-08-19

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00375	SDF	Sodium:dicarboxylate symporter family

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.3860.10	Mainly Alpha	Orthogonal Bundle	Proton glutamate symport protein	Proton glutamate symport protein	3kbcA00

2NWLA 3V8FA 2NWXA 3KBCA 1XFHA 2NWWA
chains in the KnotProt database with same CATH superfamily

2NWLA 3V8FA 2NWXA 3KBCA 1XFHA 2NWWA
chains in the KnotProt database with same CATH topology

2NWLA 3V8FA 2NWXA 3KBCA 1XFHA 2NWWA
chains in the KnotProt database with same CATH homology

#chains in the KnotProt database with same CATH superfamily
 2NWL A;  3V8F A;  2NWX A;  3KBC A;  1XFH A;  2NWW A; 
#chains in the KnotProt database with same CATH topology
 2NWL A;  3V8F A;  2NWX A;  3KBC A;  1XFH A;  2NWW A; 
#chains in the KnotProt database with same CATH homology
 2NWL A;  3V8F A;  2NWX A;  3KBC A;  1XFH A;  2NWW A;

4P19A 4P1AA 4P3JA 4P6HA
similar chains in the KnotProt database (40% sequence similarity)

6X12A 6X13A 6X14A 6X15A 6X16A
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
4P19 A; 4P1A A; 4P3J A; 4P6H A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
6X12 A; 6X13 A; 6X14 A; 6X15 A; 6X16 A;

3KBCA

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁