4ZDG | Genus

Total Genus 41

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	41
sequence length	196
structure length	196
Chain Sequence	DDNINTLWTGVNPTEANCQMMDSSESNDCKLILTLVKTGALVTAFVYVIGVSNNFNMLTTYRNINFTAELFFDSAGNLLTSLSSLKTPLNHKSGQNMATGAITNAKSFMPSTTAYPFNNNSRENYIYGTCHYTASDHTAFPIDISVMLNQRAIRADTSYCIRITWSWNTGDAPEGQTSATTLVTSPFTFYYIREDD

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__31851927582584594__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__31851927582584594__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4ZDG/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__31851927582584594__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"31851927582584594","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4ZDG/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__31851927582584594__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0129e094da184a4cf54715/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0129e094da184a4cf54715/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0129e094da184a4cf54715/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/5d0129e094da184a4cf54715/pdb.gz): 233 ms

reading 196 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

196 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:195});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	Viral protein
source organism	Human adenovirus 14p1
publication title	Intracellular Signaling and Desmoglein 2 Shedding Triggered by Human Adenoviruses Ad3, Ad14, and Ad14P1. pubmed doi rcsb
molecule keywords	Fiber protein
total genus	41
structure length	196
sequence length	196
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2015-04-17

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00541	Adeno_knob	Adenoviral fibre protein (knob domain)

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.90.10	Mainly Beta	Sandwich	Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)	Adenovirus pIV-related, attachment domain	4zdgA00

2QLKA 2WBWA 1QHVA 1P6AA 3L89A 4K6WA 4K6VA 3CNCA 4XQAA 2BZVA 2J1KC 4ZDGA 2WGTA 2WGUA 3F0YA 3L88A 1KNBA 2O39A 1UXEA 3O8EA 4ATZA 4WYJA 1UXAA 3QNDA 4LIYA 1KACA 1NOBA 1QIUA 2J12A 4XQBA 1UXBA 3N0IA 3EXWA 1H7ZA 2W9LC 3EXVA 4K6UA 4XL8A 1P69A 2WSTA 2BZUA 2WBVA 4K6TA 2J2JA 3BQ4A
chains in the Genus database with same CATH superfamily

2OJ6A 3ZPFA 2QLKA 2WBWA 2BT7A 1QHVA 1P6AA 3L89A 4K6WA 4K6VA 3CNCA 4ODBA 4XQAA 2BZVA 2JJLA 2J1KC 4ZDGA 2WGTA 4GU4A 2WGUA 4GU3A 3F0YA 3L88A 1KNBA 2O39A 1UXEA 3O8EA 4ATZA 4WYJA 1UXAA 3EOYA 4D63A 3QNDA 4LIYA 2VRSA 1KACA 2J2JA 1NOBA 1QIUA 2J12A 4XQBA 1UXBA 3N0IA 2VTWA 2BT8A 3EXWA 1H7ZA 2W9LC 3EXVA 3S6XA 4D62A 2OJ5A 4XC5A 5MHSA 1KKEA 4K6UA 4XL8A 1P69A 2WSTA 3ZPEA 2IUNA 2BZUA 2WBVA 4K6TA 2BSFA 2IUMA 3BQ4A 4CW8A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2QLK A;  2WBW A;  1QHV A;  1P6A A;  3L89 A;  4K6W A;  4K6V A;  3CNC A;  4XQA A;  2BZV A;  2J1K C;  4ZDG A;  2WGT A;  2WGU A;  3F0Y A;  3L88 A;  1KNB A;  2O39 A;  1UXE A;  3O8E A;  4ATZ A;  4WYJ A;  1UXA A;  3QND A;  4LIY A;  1KAC A;  1NOB A;  1QIU A;  2J12 A;  4XQB A;  1UXB A;  3N0I A;  3EXW A;  1H7Z A;  2W9L C;  3EXV A;  4K6U A;  4XL8 A;  1P69 A;  2WST A;  2BZU A;  2WBV A;  4K6T A;  2J2J A;  3BQ4 A; 
#chains in the Genus database with same CATH topology
 2OJ6 A;  3ZPF A;  2QLK A;  2WBW A;  2BT7 A;  1QHV A;  1P6A A;  3L89 A;  4K6W A;  4K6V A;  3CNC A;  4ODB A;  4XQA A;  2BZV A;  2JJL A;  2J1K C;  4ZDG A;  2WGT A;  4GU4 A;  2WGU A;  4GU3 A;  3F0Y A;  3L88 A;  1KNB A;  2O39 A;  1UXE A;  3O8E A;  4ATZ A;  4WYJ A;  1UXA A;  3EOY A;  4D63 A;  3QND A;  4LIY A;  2VRS A;  1KAC A;  2J2J A;  1NOB A;  1QIU A;  2J12 A;  4XQB A;  1UXB A;  3N0I A;  2VTW A;  2BT8 A;  3EXW A;  1H7Z A;  2W9L C;  3EXV A;  3S6X A;  4D62 A;  2OJ5 A;  4XC5 A;  5MHS A;  1KKE A;  4K6U A;  4XL8 A;  1P69 A;  2WST A;  3ZPE A;  2IUN A;  2BZU A;  2WBV A;  4K6T A;  2BSF A;  2IUM A;  3BQ4 A;  4CW8 A; 
#chains in the Genus database with same CATH homology
 2QLK A;  2WBW A;  1QHV A;  1P6A A;  3L89 A;  4K6W A;  4K6V A;  3CNC A;  4XQA A;  2BZV A;  2J1K C;  4ZDG A;  2WGT A;  2WGU A;  3F0Y A;  3L88 A;  1KNB A;  2O39 A;  1UXE A;  3O8E A;  4ATZ A;  4WYJ A;  1UXA A;  3QND A;  4LIY A;  1KAC A;  1NOB A;  1QIU A;  2J12 A;  4XQB A;  1UXB A;  3N0I A;  3EXW A;  1H7Z A;  2W9L C;  3EXV A;  4K6U A;  4XL8 A;  1P69 A;  2WST A;  2BZU A;  2WBV A;  4K6T A;  2J2J A;  3BQ4 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...

4ZDGA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations