2W2D | Genus

Total Genus 130

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	130
sequence length	423
structure length	423
Chain Sequence	ALNLQCIKVNNWDLFFSPSEDNFTNDLNKGEEITSDTNIEAAEENISLDLIQQYYLTFNFDNEPENISIENLSSDIIGQLELMPNIERFPNGKKYELDKYTMFHYLRAQEFEHGKSRIALTNSVNEALLNPSRVYTFFSSDYVKKVNKATEAAMFLGWVEQLVYDFTDETSEVSTTDKIADITIIIPYIGPALNIGNMLYKDDFVGALIFSGAVILLEFIPEIAIPVLGTFALVSYIANKVLTVQTIDNALSKRNEKWDEVYKYIVTNWLAKVNTQIDLIRKKMKEALENQAEATKAIINYQYNQYTEEEKNNINFNIDDLSSKLNESINKAMININKFLNQCSVSYLMNSMIPYGVKRLEDFDASLKDALLKYIYDNRGTLIGQVDRLKDKVNNTLSTDIPFQLSKYVDNQRLLSTFTEYIK

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

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Viewer cachePut cache://localLOAD_/file/5cfdbad71b82839bd6138b49/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5cfdbad71b82839bd6138b49/pdb.gz): 2430 ms

reading 423 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

423 atoms created

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

Time for creating model: 26 ms

Adding embedded #jmolscript: select ({0:422});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

molecule tags	Hydrolase
source organism	Clostridium botulinum
publication title	Crystal Structure of a Catalytically Active, Non-Toxic Endopeptidase Derivative of Clostridium Botulinum Toxin A. pubmed doi rcsb
molecule keywords	BOTULINUM NEUROTOXIN A LIGHT CHAIN
total genus	130
structure length	423
sequence length	423
chains with identical sequence	D
ec nomenclature	ec 3.4.24.69: Bontoxilysin.
pdb deposition date	2008-10-29

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

cath code	Class	Architecture	Topology	Homology	Domain
1.20.1120.10	Mainly Alpha	Up-down Bundle	Clostridium botulinum neurotoxin B, "coiled-coil" domain	Clostridium botulinum neurotoxin b, "coiled-coil" domain	2w2dB00

4ZKTB 3ZUQA 2NP0A 3VUOA 2XHLB 1I1EA 1F31A 3V0AB 1S0GA 1G9DA 3V0AA 3ZURA 3ZUSA 1G9BA 1S0EA 1G9CA 1S0BA 5BQMB 3FFZA 2NYYA 1G9AA 2W2DB 1EPWA 5BQNA 1S0DA 1S0CA 2NZ9A 3V0BB 3V0BA 1S0FA 3BTAA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 4ZKT B;  3ZUQ A;  2NP0 A;  3VUO A;  2XHL B;  1I1E A;  1F31 A;  3V0A B;  1S0G A;  1G9D A;  3V0A A;  3ZUR A;  3ZUS A;  1G9B A;  1S0E A;  1G9C A;  1S0B A;  5BQM B;  3FFZ A;  2NYY A;  1G9A A;  2W2D B;  1EPW A;  5BQN A;  1S0D A;  1S0C A;  2NZ9 A;  3V0B B;  3V0B A;  1S0F A;  3BTA A; 
#chains in the Genus database with same CATH topology
 4ZKT B;  3ZUQ A;  2NP0 A;  3VUO A;  2XHL B;  1I1E A;  1F31 A;  3V0A B;  1S0G A;  1G9D A;  3V0A A;  3ZUR A;  3ZUS A;  1G9B A;  1S0E A;  1G9C A;  1S0B A;  5BQM B;  3FFZ A;  2NYY A;  1G9A A;  2W2D B;  1EPW A;  5BQN A;  1S0D A;  1S0C A;  2NZ9 A;  3V0B B;  3V0B A;  1S0F A;  3BTA A; 
#chains in the Genus database with same CATH homology
 4ZKT B;  3ZUQ A;  2NP0 A;  3VUO A;  2XHL B;  1I1E A;  1F31 A;  3V0A B;  1S0G A;  1G9D A;  3V0A A;  3ZUR A;  3ZUS A;  1G9B A;  1S0E A;  1G9C A;  1S0B A;  5BQM B;  3FFZ A;  2NYY A;  1G9A A;  2W2D B;  1EPW A;  5BQN A;  1S0D A;  1S0C A;  2NZ9 A;  3V0B B;  3V0B A;  1S0F A;  3BTA A;

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similar chains in the Genus database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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2W2DB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization