3GYQ | KnotProt

Genus: 63

Knot K +3₁

script 1 started

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JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__5402282995681165__ initializing

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AppletRegistry.checkIn(jmolApplet1__5402282995681165__)

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

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appletId:jmolApplet1 (signed)

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defaults = "Jmol"

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backgroundColor = "white"

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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__5402282995681165__ 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	187-228	42	1-186, 229-261			186	33	knot

Chain Sequence

ANPSDPAVQRIIDVTKPSRSNIKTTLIEDVEPLMHSIAAGVEFIEVYGSDSSPFPSELLDLCGRQNIPVRLIDSSIVNQLFKGERKAKTFGIARVPRPARFGDIASRRGDVVVLDGVKIVGNIGAIVRTSLALGASGIILVDSDITSIADRRLQRASRGYVFSLPVVLSGREEAIAFIRDSGMQLMTLKADGDISVKELGDNPDRLALLFGSEKGGPSDLFEEASSASVSIPMMSQTESLNVSVSLGIALHERIDRNLAAN

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__5402282995681165__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__5402282995681165__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/3GYQ/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__5402282995681165__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"5402282995681165","bgcolor":"white" }

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

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Jmol applet jmolApplet0__5402282995681165__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/3gyq/A/3gyq_A.pdb.gz

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3gyq/A/3gyq_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/3gyq/A/3gyq_A.pdb.gz): 428 ms

reading 261 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

261 atoms created

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

Time for creating model: 44 ms

Adding embedded #jmolscript: select ({0:260});backbone only;select *;

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cartoonsFancy = true

sheetSmoothing = 1.0

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antialiasDisplay = true

Script completed

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

loadScript /static/js/j2s/J/render/MeshRenderer.js

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

Viewer cachePut cache://localLOAD_/static/knot_data/3gyq/A/3gyq_A.pdb.gz

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/3gyq/A/3gyq_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/3gyq/A/3gyq_A.pdb.gz): 25 ms

reading 261 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

261 atoms created

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

Time for creating model: 30 ms

Adding embedded #jmolscript: select ({0:260});backbone only;select *;

platformSpeed = 7

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

specularPower = 9

ambientPercent = 20

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	2.1	186-229	44	1-185, 230-261			185	32	knot
view details	2.1	185-226	42	1-184	232-261	227-231	184	30	slipknot
view details	3.1	187-229	43	230-261	1-185	186-186	185	31	slipknot
view details	3.1	188-241	54		1-186, 248-261	187-187, 242-247	186	14	slipknot
view details	2.1	188-247	60		1-186, 254-261	187-187, 248-253	186	8	slipknot

sequence length	261
structure length	261
publication title	Structure of the thiostrepton-resistance methyltransferase-S-adenosyl-L-methionine complex and its interaction with ribosomal RNA pubmed doi rcsb
molecule tags	Transferase
molecule keywords	rRNA (adenosine-2'-O-)-methyltransferase
source organism	Streptomyces cyaneus
total genus	Genus: 63
ec nomenclature	ec 2.1.1.230: 23S rRNA (adenosine(1067)-2'-O)-methyltransferase.
pdb deposition date	2009-04-04
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00588	SpoU_methylase	SpoU rRNA Methylase family

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30; Chain: A;	60s Ribosomal Protein L30; Chain: A;	3gyqA01
3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	3gyqA02

1O6DA 1J85A 1VH0A 3NK7A 3KNUA 3ONPA 3AI9X 3IC6A 2QMMA 3AIAA 4FAKA 4IG6A 1UAMA 1VHKA 3IEFA 1NS5A 2O3AA 2YY8A 1UALA 2HA8A 3KTYA 1X7PA 1TO0A 3DCMX 4CNEB 1GZ0A 4E8BA 4CNFB 3L8UA 1X7OA 3AXZA 1V6ZA 3GYQA 2I6DA 1UAKA 1ZJRA 2CX8A 4H3YA 1NXZA 3NK6A 2Z0YA 1K3RA 3QUVA 2QWVA 1UAJA 3ILKA 4CNGB 3KY7A 3N4JA 3N4KA 1MXIA 1V2XA 1P9PA 4H3ZA 1VHYA 3E5YA
chains in the KnotProt database with same CATH superfamily

#chains in the KnotProt database with same CATH superfamily
 1O6D A;  1J85 A;  1VH0 A;  3NK7 A;  3KNU A;  3ONP A;  3AI9 X;  3IC6 A;  2QMM A;  3AIA A;  4FAK A;  4IG6 A;  1UAM A;  1VHK A;  3IEF A;  1NS5 A;  2O3A A;  2YY8 A;  1UAL A;  2HA8 A;  3KTY A;  1X7P A;  1TO0 A;  3DCM X;  4CNE B;  1GZ0 A;  4E8B A;  4CNF B;  3L8U A;  1X7O A;  3AXZ A;  1V6Z A;  3GYQ A;  2I6D A;  1UAK A;  1ZJR A;  2CX8 A;  4H3Y A;  1NXZ A;  3NK6 A;  2Z0Y A;  1K3R A;  3QUV A;  2QWV A;  1UAJ A;  3ILK A;  4CNG B;  3KY7 A;  3N4J A;  3N4K A;  1MXI A;  1V2X A;  1P9P A;  4H3Z A;  1VHY A;  3E5Y A; 
#chains in the KnotProt database with same CATH topology
 1O6D A;  1J85 A;  1VH0 A;  3NK7 A;  3KNU A;  3ONP A;  3AI9 X;  3IC6 A;  2QMM A;  3AIA A;  4FAK A;  4IG6 A;  1UAM A;  1VHK A;  3IEF A;  1NS5 A;  2O3A A;  2YY8 A;  1UAL A;  2HA8 A;  3KTY A;  1X7P A;  1TO0 A;  3DCM X;  4CNE B;  1GZ0 A;  4E8B A;  4CNF B;  3L8U A;  1X7O A;  3AXZ A;  1V6Z A;  3GYQ A;  2I6D A;  1UAK A;  1ZJR A;  2CX8 A;  4H3Y A;  1NXZ A;  3NK6 A;  2Z0Y A;  1K3R A;  3QUV A;  2QWV A;  1UAJ A;  3ILK A;  4CNG B;  3KY7 A;  3N4J A;  3N4K A;  1MXI A;  1V2X A;  1P9P A;  4H3Z A;  1VHY A;  3E5Y A; 
#chains in the KnotProt database with same CATH homology
 1O6D A;  1J85 A;  1VH0 A;  3NK7 A;  3KNU A;  3ONP A;  3AI9 X;  3IC6 A;  2QMM A;  3AIA A;  4FAK A;  4IG6 A;  1UAM A;  1VHK A;  3IEF A;  1NS5 A;  2O3A A;  2YY8 A;  1UAL A;  2HA8 A;  3KTY A;  1X7P A;  1TO0 A;  3DCM X;  4CNE B;  1GZ0 A;  4E8B A;  4CNF B;  3L8U A;  1X7O A;  3AXZ A;  1V6Z A;  3GYQ A;  2I6D A;  1UAK A;  1ZJR A;  2CX8 A;  4H3Y A;  1NXZ A;  3NK6 A;  2Z0Y A;  1K3R A;  3QUV A;  2QWV A;  1UAJ A;  3ILK A;  4CNG B;  3KY7 A;  3N4J A;  3N4K A;  1MXI A;  1V2X A;  1P9P A;  4H3Z A;  1VHY A;  3E5Y 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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3GYQA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁