2WGU | Genus

Total Genus 44

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	44
sequence length	185
structure length	185
Chain Sequence	YDTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE

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__8273010221140846__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8273010221140846__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2WGU/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__8273010221140846__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"8273010221140846","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2WGU/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__8273010221140846__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfdc82220b281166df21571/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfdc82220b281166df21571/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfdc82220b281166df21571/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/5cfdc82220b281166df21571/pdb.gz): 273 ms

reading 185 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

185 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:184});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 37
publication title	Design, Synthesis, and Evaluation of N-Acyl Modified Sialic Acids as Inhibitors of Adenoviruses Causing Epidemic Keratoconjunctivitis. pubmed doi rcsb
molecule keywords	FIBER PROTEIN
total genus	44
structure length	185
sequence length	185
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2009-04-27

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	2wguA00

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

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

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

2WGUA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations