3KNU | KnotProt

Genus: 51

Knot K +3₁

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

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callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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Jmol applet jmolApplet1__3617922458201837__ 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	86-130	45	1-85, 131-212			85	82	knot

Chain Sequence

SMIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFA-----TVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVIEYPQY---------------TRPASWKGMEVPEVLLTGNHGEIEKWRRNASL

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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Jmol JavaScript applet jmolApplet0__3617922458201837__ initializing

Jmol getValue debug null

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AppletRegistry.checkIn(jmolApplet0__3617922458201837__)

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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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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

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Jmol getValue EVALCallback null

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Jmol getValue MESSAGECallback null

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Jmol getValue PICKCallback null

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Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

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Viewer cachePut cache://localLOAD_/static/knot_data/3knu/A/3knu_A.pdb.gz

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/3knu/A/3knu_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/3knu/A/3knu_A.pdb.gz): 657 ms

reading 192 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

192 atoms created

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

Time for creating model: 32 ms

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Script completed

Jmol script terminated

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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	81-127	47	1-80, 128-192			80	65	knot
view details				2.1	78-123	46	1-77	130-192	124-129	77	63	slipknot

sequence length	212
structure length	192
publication title	Crystal structure of tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum rcsb
molecule tags	Transferase
molecule keywords	tRNA (guanine-N(1)-)-methyltransferase
source organism	Anaplasma phagocytophilum
missing residues	44-48, 161-175
total genus	Genus: 51
ec nomenclature	ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date	2009-11-12
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01746	tRNA_m1G_MT	tRNA (Guanine-1)-methyltransferase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	3knuA01

1O6DA 1J85A 1VH0A 3NK7A 3KNUA 3ONPA 3AI9X 3IC6A 2QMMA 3AIAA 4FAKA 4IG6A 1UAMA 1VHKA 3IEFA 1NS5A 2O3AA 2YY8A 1UALA 2HA8A 3KTYA 1TO0A 1X7PA 3DCMX 4CNEB 1GZ0A 4E8BA 4CNFB 3L8UA 1X7OA 3AXZA 1V6ZA 1ZJRA 1UAKA 2CX8A 2I6DA 3GYQA 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;  1TO0 A;  1X7P A;  3DCM X;  4CNE B;  1GZ0 A;  4E8B A;  4CNF B;  3L8U A;  1X7O A;  3AXZ A;  1V6Z A;  1ZJR A;  1UAK A;  2CX8 A;  2I6D A;  3GYQ 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;  1TO0 A;  1X7P A;  3DCM X;  4CNE B;  1GZ0 A;  4E8B A;  4CNF B;  3L8U A;  1X7O A;  3AXZ A;  1V6Z A;  1ZJR A;  1UAK A;  2CX8 A;  2I6D A;  3GYQ 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;  1TO0 A;  1X7P A;  3DCM X;  4CNE B;  1GZ0 A;  4E8B A;  4CNF B;  3L8U A;  1X7O A;  3AXZ A;  1V6Z A;  1ZJR A;  1UAK A;  2CX8 A;  2I6D A;  3GYQ 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;

3IEFA 3QUVA 4H3YA 4H3ZA 4IG6A
similar chains in the KnotProt database (40% sequence similarity)

8FCHA 8FCIA 8SH4A 8TXAA
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
3IEF A; 3QUV A; 4H3Y A; 4H3Z A; 4IG6 A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
8FCH A; 8FCI A; 8SH4 A; 8TXA A;

3KNUA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁