4H3Y | KnotProt

Genus: 77

Knot K +3₁

script 1 started

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AppletRegistry.checkIn(jmolApplet1__967178042047939__)

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setting document base to "https://knotprot.cent.uw.edu.pl/view/4H3Y/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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Jmol getValue emulate null

defaults = "Jmol"

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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__967178042047939__ 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	91-135	45	1-90, 136-255			90	120	knot

Chain Sequence

SMQFDIVTLFPDMFRALTDWGITSRAAKQERYGLRTWNPRDFTTDNYRTIDDRPYGGGPGMVMLARPLEDAINAAKAAQAEQGIGGARVVMMSPQGATLNHDKVMRFAAEPGLILLCGRYEAIDQRLIDRVVDEEVSLGDFVLSGGELPAMALIDAVVRHLPGVLNDAQSAVQDSFVDGLLDCPHYTRPEEYDGVRVPDVLLGGHHAEIEQWRRREALRNTWLKRPDLIVQARKNKLLSRADEAWLASLAKDASK

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__967178042047939__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__967178042047939__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/4H3Y/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__967178042047939__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/4h3y/A/4h3y_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/4h3y/A/4h3y_A.pdb.gz

Viewer cachePut cache://localLOAD_/static/knot_data/4h3y/A/4h3y_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/4h3y/A/4h3y_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/4h3y/A/4h3y_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/4h3y/A/4h3y_A.pdb.gz): 937 ms

reading 255 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

255 atoms created

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

Time for creating model: 34 ms

Adding embedded #jmolscript: select ({0:254});backbone only;select *;

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cartoonsFancy = true

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traceAlpha = true

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

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

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loadScript /static/js/j2s/J/g3d/HermiteRenderer.js

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

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

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

FileManager.getAtomSetCollectionFromFile(/static/knot_data/4h3y/A/4h3y_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/4h3y/A/4h3y_A.pdb.gz): 18 ms

reading 255 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

255 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:254});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				3.1	91-136	46	1-90, 137-255			90	119	knot

sequence length	255
structure length	255
publication title	Combining functional and structural genomics to sample the essential Burkholderia structome. pubmed doi rcsb
molecule tags	Transferase
molecule keywords	tRNA (guanine-N(1)-)-methyltransferase
source organism	Burkholderia phymatum
total genus	Genus: 77
ec nomenclature	ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date	2012-09-14
KnotProt deposition date	2014-08-19

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
1.10.1270.20	Mainly Alpha	Orthogonal Bundle	Trp Operon Repressor; Chain A	tRNA(m1g37)methyltransferase, domain 2	4h3yA02
3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	4h3yA01

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

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

1UAJA 1UAKA 1UALA 1UAMA 3AXZA 4H3ZA 4YQDA 4YVGA 4YVHA
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)
1UAJ A; 1UAK A; 1UAL A; 1UAM A; 3AXZ A; 4H3Z A; 4YQD A; 4YVG A; 4YVH A; 
#similar chains, but unknotted

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

4H3YA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁