2BDS | Genus

Total Genus 3

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	3
sequence length	43
structure length	43
Chain Sequence	AAPCFCSGKPGRGDLWILRGTCPGGYGYTSNCYKWPNICCYPH

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

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__7845347910123106__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__7845347910123106__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2BDS/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__7845347910123106__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"7845347910123106","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2BDS/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__7845347910123106__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfca933e0f6540cec760ec1/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfca933e0f6540cec760ec1/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfca933e0f6540cec760ec1/pdb.gz)

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

The Resolver thinks Pdb

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

Time for openFile(/file/5cfca933e0f6540cec760ec1/pdb.gz): 1026 ms

reading 43 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

43 atoms created

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

Time for creating model: 13 ms

Adding embedded #jmolscript: select ({0:42});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

Chord Diagram

molecule tags	Anti-hypertensive, anti-viral protein
source organism	Anemonia sulcata
publication title	Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. pubmed doi rcsb
molecule keywords	BDS-I
total genus	3
structure length	43
sequence length	43
ec nomenclature
pdb deposition date	1988-11-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF07936	Defensin_4	Potassium-channel blocking toxin

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

cath code	Class	Architecture	Topology	Homology	Domain
2.20.20.10	Mainly Beta	Single Sheet	Anthopleurin-A	Anthopleurin-A	2bdsA00

3D4UB 1ZLIB 2SH1A 1BDSA 1SH1A 2MUBA 2RNGA 1AHLA 1ZUEA 1D6BA 1B8WA 1ZLHB 2MN3A 1ZUFA 1H5OA 1APFA 1ATXA 2BDSA 1Z99A 3LMSB 1WXNA 2JTOA 2H9XA 1WQKA 4GV5A 2K2XA 1SHIA
chains in the Genus database with same CATH superfamily

3D4UB 4YIRA 2QSHA 2B9KA 1ZLIB 2IKEA 2DLAA 2SH1A 3KEZA 1BDSA 1SH1A 2MUBA 2HJEA 3C30A 3MYVA 2RNGA 1AHLA 1ZUEA 2XXLA 1D6BA 1B8WA 1ZLHB 2MN3A 1ZUFA 1H5OA 2IKDA 3MCXA 2QSFA 1APFA 1ATXA 2BDSA 2QSGA 1GL9B 1Z99A 1ZHHB 1EL6A 2HJ9C 3IF4A 3LMSB 2JR3A 1WXNA 2JTOA 3C38A 2H9XA 1GKUB 1WQKA 4GV5A 2K2XA 1SHIA
chains in the Genus database with same CATH topology

3D4UB 4YIRA 2QSHA 2B9KA 1ZLIB 2IKEA 2DLAA 2SH1A 3KEZA 1BDSA 1SH1A 2MUBA 2HJEA 3C30A 3MYVA 2RNGA 1AHLA 1ZUEA 2XXLA 1D6BA 1B8WA 1ZLHB 2MN3A 1ZUFA 1H5OA 2IKDA 3MCXA 2QSFA 1APFA 1ATXA 2BDSA 2QSGA 1Z99A 1ZHHB 2HJ9C 3LMSB 2JR3A 1WXNA 2JTOA 3C38A 2H9XA 1WQKA 4GV5A 2K2XA 1SHIA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3D4U B;  1ZLI B;  2SH1 A;  1BDS A;  1SH1 A;  2MUB A;  2RNG A;  1AHL A;  1ZUE A;  1D6B A;  1B8W A;  1ZLH B;  2MN3 A;  1ZUF A;  1H5O A;  1APF A;  1ATX A;  2BDS A;  1Z99 A;  3LMS B;  1WXN A;  2JTO A;  2H9X A;  1WQK A;  4GV5 A;  2K2X A;  1SHI A; 
#chains in the Genus database with same CATH topology
 3D4U B;  4YIR A;  2QSH A;  2B9K A;  1ZLI B;  2IKE A;  2DLA A;  2SH1 A;  3KEZ A;  1BDS A;  1SH1 A;  2MUB A;  2HJE A;  3C30 A;  3MYV A;  2RNG A;  1AHL A;  1ZUE A;  2XXL A;  1D6B A;  1B8W A;  1ZLH B;  2MN3 A;  1ZUF A;  1H5O A;  2IKD A;  3MCX A;  2QSF A;  1APF A;  1ATX A;  2BDS A;  2QSG A;  1GL9 B;  1Z99 A;  1ZHH B;  1EL6 A;  2HJ9 C;  3IF4 A;  3LMS B;  2JR3 A;  1WXN A;  2JTO A;  3C38 A;  2H9X A;  1GKU B;  1WQK A;  4GV5 A;  2K2X A;  1SHI A; 
#chains in the Genus database with same CATH homology
 3D4U B;  4YIR A;  2QSH A;  2B9K A;  1ZLI B;  2IKE A;  2DLA A;  2SH1 A;  3KEZ A;  1BDS A;  1SH1 A;  2MUB A;  2HJE A;  3C30 A;  3MYV A;  2RNG A;  1AHL A;  1ZUE A;  2XXL A;  1D6B A;  1B8W A;  1ZLH B;  2MN3 A;  1ZUF A;  1H5O A;  2IKD A;  3MCX A;  2QSF A;  1APF A;  1ATX A;  2BDS A;  2QSG A;  1Z99 A;  1ZHH B;  2HJ9 C;  3LMS B;  2JR3 A;  1WXN A;  2JTO A;  3C38 A;  2H9X A;  1WQK A;  4GV5 A;  2K2X A;  1SHI A;

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

2BDSA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations