1NOB | Genus

Total Genus 34

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	34
sequence length	185
structure length	185
Chain Sequence	TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE

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__210966808146466__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__210966808146466__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1NOB/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__210966808146466__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"210966808146466","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1NOB/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__210966808146466__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfba9f71b1b4784f9b3e09a/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfba9f71b1b4784f9b3e09a/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfba9f71b1b4784f9b3e09a/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/5cfba9f71b1b4784f9b3e09a/pdb.gz): 494 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

molecule tags	Viral protein
source organism	Human adenovirus 12
publication title	Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR. pubmed doi rcsb
molecule keywords	PROTEIN (FIBER KNOB PROTEIN)
total genus	34
structure length	185
sequence length	185
chains with identical sequence	B, C, D, E, F
ec nomenclature
pdb deposition date	1999-05-05

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	1nobA00

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

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

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

1NOBA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations