5LBR | KnotProt

5LBRA

Wild-type pas-gaf fragment from deinococcus radiodurans bphp collected at sacla

Image from the <span class='capital'>rcsb pdb</span> (www.rcsb.org)

Warning

Chain breaks within knot 4₁ (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.

Genus: 84

Knot K 4₁ 4₁

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setting document base to "https://knotprot.cent.uw.edu.pl/view/5lbr/A/"

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

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java.version: 2018-01-28 23:38:52 (JSmol/j2s)

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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

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Jmol getValue LOADSTRUCTCallback null

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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

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Jmol getValue popupMenu null

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Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet1__90514130384357__ 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				4₁	29-267	239	1-28, 268-316			28	49	knot

Chain Sequence

PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWP---HLSLTVHRVGELLILEFEPTELRN---------AMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAL

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__90514130384357__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__90514130384357__)

vwrOptions:

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setting document base to "https://knotprot.cent.uw.edu.pl/view/5lbr/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__90514130384357__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/5lbr/A/5lbr_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5lbr/A/5lbr_A.pdb.gz

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Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5lbr/A/5lbr_A.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5lbr/A/5lbr_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/5lbr/A/5lbr_A.pdb.gz): 1025 ms

reading 304 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

304 atoms created

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

Time for creating model: 47 ms

Adding embedded #jmolscript: select ({0:303});backbone only;select *;

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5lbr/A/5lbr_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/5lbr/A/5lbr_A.pdb.gz): 17 ms

reading 304 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

304 atoms created

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

Time for creating model: 24 ms

Adding embedded #jmolscript: select ({0:303});backbone only;select *;

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cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

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

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

Jmol script terminated

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

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	4.1	26-295	270	1-25, 296-304			25	9	knot
view details	3.2m	27-251	225	1-26	261-304	252-260	26	44	slipknot
view details	3.2m	28-263	236	1-27	296-304	264-295	27	9	slipknot
view details	4.1	24-260	237		1-12, 264-304	13-23, 261-263	12	41	slipknot
view details	3.2	30-292	263	293-304	1-25	26-29	25	11	slipknot
view details	3.2	31-294	264	295-304	1-29	30-30	29	9	slipknot

sequence length	316
structure length	304
publication title	The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography. pubmed doi rcsb
molecule tags	Transferase
molecule keywords	Bacteriophytochrome
source organism	Deinococcus radiodurans
missing residues	101-103, 125-133
total genus	Genus: 84
ec nomenclature
pdb deposition date	2016-06-17
KnotProt deposition date	2016-11-13

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

3S7NA 5L8MA 5LBRA 5NFXA
similar chains in the KnotProt database (40% sequence similarity)

6FTDA 6T3LA 6T3UA 7Z9DA 8C3IA
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
3S7N A; 5L8M A; 5LBR A; 5NFX A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
6FTD A; 6T3L A; 6T3U A; 7Z9D A; 8C3I A;

How to cite

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling

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5LBRA

Knot K 41 41

Chain Sequence

Knot K 4₁ 4₁