1UXB | Genus

Total Genus 43

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	43
sequence length	184
structure length	184
Chain Sequence	DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPEIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFDFSWSKTYENVEFETTSFTFSYIAQE

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__321179170599134__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__321179170599134__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1UXB/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__321179170599134__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"321179170599134","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1UXB/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__321179170599134__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfc394a8a696f5ebda2ab57/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfc394a8a696f5ebda2ab57/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfc394a8a696f5ebda2ab57/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/5cfc394a8a696f5ebda2ab57/pdb.gz): 787 ms

reading 184 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

184 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:183});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

molecule tags	Viral protein
source organism	Human adenovirus type 19
publication title	Crystal Structure of Species D Adenovirus Fiber Knobs and Their Sialic Acid Binding Sites pubmed doi rcsb
molecule keywords	FIBER PROTEIN
total genus	43
structure length	184
sequence length	184
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2004-02-24

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	1uxbA00

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

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

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

1UXBA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations