1TDP | Genus

Total Genus 25

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	25
sequence length	111
structure length	111
Chain Sequence	MDIKSQTLYLNLSEAYKDPEVKANEFLSKLVVQCAGKLTASNSENSYIEVISLLSRGISSYYLSHKRIIPSSMLTIYTQIQKDIKNGNIDTEKLRKYEIAKGLMSVPYIYF

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__786631715951474__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__786631715951474__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1TDP/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__786631715951474__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"786631715951474","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1TDP/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__786631715951474__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfc144189f985553e431f3b/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfc144189f985553e431f3b/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfc144189f985553e431f3b/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/5cfc144189f985553e431f3b/pdb.gz): 58 ms

reading 111 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

111 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:110});backbone only;select *;

platformSpeed = 8

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

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	Antimicrobial protein
source organism	Carnobacterium maltaromaticum
publication title	NMR Solution Structure of ImB2, a Protein Conferring Immunity to Antimicrobial Activity of the Type IIa Bacteriocin, Carnobacteriocin B2 pubmed doi rcsb
molecule keywords	carnobacteriocin B2 immunity protein
total genus	25
structure length	111
sequence length	111
ec nomenclature
pdb deposition date	2004-05-23

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF08951	EntA_Immun	Enterocin A Immunity

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

cath code	Class	Architecture	Topology	Homology	Domain
1.20.1440.50	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	Ta0600-like	1tdpA00

2QSBA 2BL7A 1TDPA 2BL8A 2FU2A 2QZGA
chains in the Genus database with same CATH superfamily

4G75A 1TDPA 2QZGA 3DA3A 2ZW3A 2XTRA 4G76A 3JSBA 2BL8A 3DO9A 2JB1A 2MJFB 2JAEA 1YO7A 3FBVA 4PL5A 2RADA 4PL3A 3Q8DA 2XMXA 4HEA1 3DA4A 4PL4A 3FNBA 2ETDA 3IAS1 2HGKA 2F66B 2IP6A 2A2CA 2ZRRA 4JCVE 2JB2A 2JB3A 2YFAA 2FU2A 5HGIA 3IAM1 2KKMA 5LNK1 4O1PA 3LJ2A 2CAZB 4Z7GA 3F4MA 2RIOA 4I1TA 4OAVB 3SDJA 3LJ0A 3VA9A 4OAUC 1U5KA 4YZ9A 2FEFA 3LJ1A 4YZCA 2BL7A 4NV5A 4O1OA 1SJ8A 1W3SA 3I9V1 3L0IA 4Q9VA 2V6EA 2F6MB 1JQOA 2L1LB 3B55A 4U6RA 4AS2A 4DWLA 2YFBA 3KP9A 2A2DA 4Z7HA 3P23A 2K19A 2FUG1 3AJFA 3FVVA 2GSCA 4AS3A 2QSBA 2E8GA 4HFVA 4GXTA 4YZDA 3UITA 2V1CC 2P22B 2QGMA 2XTQA 4NV2A 2JBWA 2RLDA
chains in the Genus database with same CATH topology

2QSBA 2BL7A 1TDPA 2BL8A 2FU2A 2QZGA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2QSB A;  2BL7 A;  1TDP A;  2BL8 A;  2FU2 A;  2QZG A; 
#chains in the Genus database with same CATH topology
 4G75 A;  1TDP A;  2QZG A;  3DA3 A;  2ZW3 A;  2XTR A;  4G76 A;  3JSB A;  2BL8 A;  3DO9 A;  2JB1 A;  2MJF B;  2JAE A;  1YO7 A;  3FBV A;  4PL5 A;  2RAD A;  4PL3 A;  3Q8D A;  2XMX A;  4HEA 1;  3DA4 A;  4PL4 A;  3FNB A;  2ETD A;  3IAS 1;  2HGK A;  2F66 B;  2IP6 A;  2A2C A;  2ZRR A;  4JCV E;  2JB2 A;  2JB3 A;  2YFA A;  2FU2 A;  5HGI A;  3IAM 1;  2KKM A;  5LNK 1;  4O1P A;  3LJ2 A;  2CAZ B;  4Z7G A;  3F4M A;  2RIO A;  4I1T A;  4OAV B;  3SDJ A;  3LJ0 A;  3VA9 A;  4OAU C;  1U5K A;  4YZ9 A;  2FEF A;  3LJ1 A;  4YZC A;  2BL7 A;  4NV5 A;  4O1O A;  1SJ8 A;  1W3S A;  3I9V 1;  3L0I A;  4Q9V A;  2V6E A;  2F6M B;  1JQO A;  2L1L B;  3B55 A;  4U6R A;  4AS2 A;  4DWL A;  2YFB A;  3KP9 A;  2A2D A;  4Z7H A;  3P23 A;  2K19 A;  2FUG 1;  3AJF A;  3FVV A;  2GSC A;  4AS3 A;  2QSB A;  2E8G A;  4HFV A;  4GXT A;  4YZD A;  3UIT A;  2V1C C;  2P22 B;  2QGM A;  2XTQ A;  4NV2 A;  2JBW A;  2RLD A; 
#chains in the Genus database with same CATH homology
 2QSB A;  2BL7 A;  1TDP A;  2BL8 A;  2FU2 A;  2QZG 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...

1TDPA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations