5HK5 | KnotProt

Cysteine knot

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 jmolApplet3 start applet null

Jmol JavaScript applet jmolApplet3__690199057221938__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet3__690199057221938__)

vwrOptions:

{ "name":"jmolApplet3","applet":true,"documentBase":"https://knotprot.cent.uw.edu.pl/view/5hk5/C/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet3__690199057221938__","codePath":"https:/static/js/j2s/","display":"jmolApplet3_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"690199057221938","bgcolor":"white" }

setting document base to "https://knotprot.cent.uw.edu.pl/view/5hk5/C/"

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:jmolApplet3 (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 jmolApplet3__690199057221938__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/5hk5/C/5hk5_C_cysteine_knot.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/5hk5/C/5hk5_C_cysteine_knot.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/5hk5/C/5hk5_C_cysteine_knot.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/5hk5/C/5hk5_C_cysteine_knot.pdb.gz): 391 ms

reading 105 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

105 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:104});backbone only;select *;

platformSpeed = 7

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 Cysteine knot data interpretation Full screen

				Loop	Piercing
view details				48-c-52-b-119-c-117	19-b-85

Chain Sequence

KARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR

sequence length	105
structure length	105
publication title	Structure of Gremlin-2 in Complex with GDF5 Gives Insight into DAN-Family-Mediated BMP Antagonism. pubmed doi rcsb
molecule tags	Cytokine
molecule keywords	Gremlin-2
source organism	Mus musculus
ec nomenclature
pdb deposition date	2016-01-13

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

1WAQA 3EVSB 5HK5A 6Z3GA
similar chains in the KnotProt database (40% sequence similarity)

7ZJFA 8BWLA 8BWMA 8BWNA 8E3GB
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
1WAQ A; 3EVS B; 5HK5 A; 6Z3G A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
7ZJF A; 8BWL A; 8BWM A; 8BWN A; 8E3G B;

5HK5C

Cysteine knot

Chain Sequence