2I6D | KnotProt

Genus: 73

Knot K +3₁

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

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language=en_US

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Jmol applet jmolApplet1__073530016072712__ 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	179-221	43	1-178, 222-255			178	34	knot

Chain Sequence

AMLSANQIKFLRSLRERKYRLREQAFAVEGPKLVGEMLPFYRCRMLVGTAAMLRAVSTPHDAEVVELPESFDFKRISTQTTPQPLMAVFDLPAEPEPVVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPASGLSV----ESLNVAIATAILCSEWRRRS

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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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__073530016072712__ initializing

Jmol getValue debug null

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Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__073530016072712__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/2I6D/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

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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 MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

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Jmol applet jmolApplet0__073530016072712__ ready

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Viewer cachePut cache://localLOAD_/static/knot_data/2i6d/A/2i6d_A.pdb.gz

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/2i6d/A/2i6d_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/2i6d/A/2i6d_A.pdb.gz): 787 ms

reading 251 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

251 atoms created

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

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/2i6d/A/2i6d_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/2i6d/A/2i6d_A.pdb.gz): 16 ms

reading 251 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

251 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:250});backbone only;select *;

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cartoonsFancy = 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	3.1	178-224	47	1-177, 225-251			177	27	knot
view details	2.1	178-218	41	1-177	225-251	219-224	177	27	slipknot
view details	3.1	179-224	46	225-251	1-177	178-178	177	26	slipknot
view details	3.1	181-234	54		1-178, 242-251	179-180, 235-241	178	10	slipknot
view details	3.1	180-242	63	243-251	1-178	179-179	178	8	slipknot
view details	3.1	181-243	63		1-179, 251-251	180-180, 244-250	179	1	slipknot

sequence length	255
structure length	251
publication title	The structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis. rcsb
molecule tags	Transferase
molecule keywords	RNA methyltransferase, TrmH family
source organism	Porphyromonas gingivalis
missing residues	232-235
total genus	Genus: 73
ec nomenclature	ec 2.1.1.-:
pdb deposition date	2006-08-28
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;	2i6dA01
3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	2i6dA02

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

#chains in the KnotProt database with same CATH superfamily
 3NK7 A;  3KTY A;  3AIA A;  1VHY A;  2I6D A;  3DCM X;  3N4J A;  3ILK A;  4IG6 A;  3ONP A;  1X7O A;  1UAJ A;  3N4K A;  3AXZ A;  3L8U A;  2QWV A;  4E8B A;  2CX8 A;  3E5Y A;  1NXZ A;  1ZJR A;  1TO0 A;  4H3Y A;  1VHK A;  1VH0 A;  1V6Z A;  4FAK A;  1GZ0 A;  2Z0Y A;  4CNG B;  3QUV A;  1K3R A;  3NK6 A;  1UAK A;  1UAL A;  3GYQ A;  3AI9 X;  3IC6 A;  4H3Z A;  2QMM A;  4CNF B;  1NS5 A;  1V2X A;  2HA8 A;  2YY8 A;  1O6D A;  3IEF A;  1X7P A;  3KY7 A;  2O3A A;  3KNU A;  1J85 A;  1P9P A;  4CNE B;  1UAM A;  1MXI A; 
#chains in the KnotProt database with same CATH topology
 3NK7 A;  3KTY A;  3AIA A;  1VHY A;  2I6D A;  3DCM X;  3N4J A;  3ILK A;  4IG6 A;  3ONP A;  1X7O A;  1UAJ A;  3N4K A;  3AXZ A;  3L8U A;  2QWV A;  4E8B A;  2CX8 A;  3E5Y A;  1NXZ A;  1ZJR A;  1TO0 A;  4H3Y A;  1VHK A;  1VH0 A;  1V6Z A;  4FAK A;  1GZ0 A;  2Z0Y A;  4CNG B;  3QUV A;  1K3R A;  3NK6 A;  1UAK A;  1UAL A;  3GYQ A;  3AI9 X;  3IC6 A;  4H3Z A;  2QMM A;  4CNF B;  1NS5 A;  1V2X A;  2HA8 A;  2YY8 A;  1O6D A;  3IEF A;  1X7P A;  3KY7 A;  2O3A A;  3KNU A;  1J85 A;  1P9P A;  4CNE B;  1UAM A;  1MXI A; 
#chains in the KnotProt database with same CATH homology
 3NK7 A;  3KTY A;  3AIA A;  1VHY A;  2I6D A;  3DCM X;  3N4J A;  3ILK A;  4IG6 A;  3ONP A;  1X7O A;  1UAJ A;  3N4K A;  3AXZ A;  3L8U A;  2QWV A;  4E8B A;  2CX8 A;  3E5Y A;  1NXZ A;  1ZJR A;  1TO0 A;  4H3Y A;  1VHK A;  1VH0 A;  1V6Z A;  4FAK A;  1GZ0 A;  2Z0Y A;  4CNG B;  3QUV A;  1K3R A;  3NK6 A;  1UAK A;  1UAL A;  3GYQ A;  3AI9 X;  3IC6 A;  4H3Z A;  2QMM A;  4CNF B;  1NS5 A;  1V2X A;  2HA8 A;  2YY8 A;  1O6D A;  3IEF A;  1X7P A;  3KY7 A;  2O3A A;  3KNU A;  1J85 A;  1P9P A;  4CNE B;  1UAM A;  1MXI 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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2I6DA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁