1TWH | KnotProt

Cysteine knot

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Jmol JavaScript applet jmolApplet3__7518607001498__ initializing

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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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Viewer cachePut cache://localLOAD_/static/knot_data/1twh/I/1twh_I_cysteine_knot.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1twh/I/1twh_I_cysteine_knot.pdb.gz

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1twh/I/1twh_I_cysteine_knot.pdb.gz)

The Resolver thinks Pdb

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Time for openFile(/static/knot_data/1twh/I/1twh_I_cysteine_knot.pdb.gz): 2849 ms

reading 121 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

121 atoms created

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

Time for creating model: 26 ms

Adding embedded #jmolscript: select ({0:120});backbone only;select *;

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

Help Cysteine knot data interpretation Full screen

				Loop	Piercing
view details				10-c-29-b-32-c-32	7-b-32

Chain Sequence

MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQF

sequence length	121
structure length	121
publication title	Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. pubmed doi rcsb
molecule tags	Transcription
molecule keywords	DNA-directed RNA polymerase II largest subunit
ec nomenclature
pdb deposition date	2004-06-30

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

cath code	Class	Architecture	Topology	Homology	Domain
2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	N-terminal domain of TfIIb	1twhI01
2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	N-terminal domain of TfIIb	1twhI02

1TWHI 1TWGI
chains in the KnotProt database with same CATH superfamily

1TWHI 1TWGI
chains in the KnotProt database with same CATH topology

1TWHI 1TWGI
chains in the KnotProt database with same CATH homology

#chains in the KnotProt database with same CATH superfamily
 1TWH I;  1TWG I; 
#chains in the KnotProt database with same CATH topology
 1TWH I;  1TWG I; 
#chains in the KnotProt database with same CATH homology
 1TWH I;  1TWG I;

None 1I50I 1I6HI 1K83I 1NIKI 1NT9I 1PQVI 1R5UI 1R9SI 1R9TI
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)

#similar chains, but unknotted
1R9T I; 
#similar chains in the pdb database (40% sequence similarity)