2QDY | Genus

Total Genus 60

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	60
sequence length	197
structure length	195
Chain Sequence	ENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLSTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT

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__965618734655957__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__965618734655957__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2QDY/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__965618734655957__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"965618734655957","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2QDY/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__965618734655957__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd7ce98c360daa5533b94f/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd7ce98c360daa5533b94f/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd7ce98c360daa5533b94f/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/5cfd7ce98c360daa5533b94f/pdb.gz): 146 ms

reading 195 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

195 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:194});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	Lyase
publication title	High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism pubmed doi rcsb
molecule keywords	Nitrile hydratase subunit alpha
total genus	60
structure length	195
sequence length	197
ec nomenclature	ec 4.2.1.84: Nitrile hydratase.
pdb deposition date	2007-06-22

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02979	NHase_alpha	Nitrile hydratase, alpha chain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.90.330.10	Alpha Beta	Alpha-Beta Complex	Nitrile Hydratase; Chain A	Nitrile hydratase alpha /Thiocyanate hydrolase gamma	2qdyA00

1UGRA 3A8GA 3VYGC 3WVDA 1AHJA 4OB0A 3QZ5A 2ZPFA 4OB1A 3X26A 1UGPA 2ZPEA 4ZGEA 2CZ1A 2AHJA 3A8LA 3X24A 1UGSA 4ZGJA 1V29A 3QYHA 3QYGA 2ZPHA 2ZPGA 4ZGDA 3VYHA 3A8MA 3QXEA 2CZ0A 3X25A 2ZCFA 1UGQA 3X20A 1IREA 4OB3A 3WVEA 2CZ7A 2ZPBA 3A8HA 2DD4C 2ZPIA 2CYZA 2QDYA 2ZZDC 3A8OA 2DD5C 2DXBC 3HHTA 4FM4A 2CZ6A 2DXCC 3X28A 2D0QA 4OB2A 3QZ9A 2DPPA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1UGR A;  3A8G A;  3VYG C;  3WVD A;  1AHJ A;  4OB0 A;  3QZ5 A;  2ZPF A;  4OB1 A;  3X26 A;  1UGP A;  2ZPE A;  4ZGE A;  2CZ1 A;  2AHJ A;  3A8L A;  3X24 A;  1UGS A;  4ZGJ A;  1V29 A;  3QYH A;  3QYG A;  2ZPH A;  2ZPG A;  4ZGD A;  3VYH A;  3A8M A;  3QXE A;  2CZ0 A;  3X25 A;  2ZCF A;  1UGQ A;  3X20 A;  1IRE A;  4OB3 A;  3WVE A;  2CZ7 A;  2ZPB A;  3A8H A;  2DD4 C;  2ZPI A;  2CYZ A;  2QDY A;  2ZZD C;  3A8O A;  2DD5 C;  2DXB C;  3HHT A;  4FM4 A;  2CZ6 A;  2DXC C;  3X28 A;  2D0Q A;  4OB2 A;  3QZ9 A;  2DPP A; 
#chains in the Genus database with same CATH topology
 1UGR A;  3A8G A;  3VYG C;  3WVD A;  1AHJ A;  4OB0 A;  3QZ5 A;  2ZPF A;  4OB1 A;  3X26 A;  1UGP A;  2ZPE A;  4ZGE A;  2CZ1 A;  2AHJ A;  3A8L A;  3X24 A;  1UGS A;  4ZGJ A;  1V29 A;  3QYH A;  3QYG A;  2ZPH A;  2ZPG A;  4ZGD A;  3VYH A;  3A8M A;  3QXE A;  2CZ0 A;  3X25 A;  2ZCF A;  1UGQ A;  3X20 A;  1IRE A;  4OB3 A;  3WVE A;  2CZ7 A;  2ZPB A;  3A8H A;  2DD4 C;  2ZPI A;  2CYZ A;  2QDY A;  2ZZD C;  3A8O A;  2DD5 C;  2DXB C;  3HHT A;  4FM4 A;  2CZ6 A;  2DXC C;  3X28 A;  2D0Q A;  4OB2 A;  3QZ9 A;  2DPP A; 
#chains in the Genus database with same CATH homology
 1UGR A;  3A8G A;  3VYG C;  3WVD A;  1AHJ A;  4OB0 A;  3QZ5 A;  2ZPF A;  4OB1 A;  3X26 A;  1UGP A;  2ZPE A;  4ZGE A;  2CZ1 A;  2AHJ A;  3A8L A;  3X24 A;  1UGS A;  4ZGJ A;  1V29 A;  3QYH A;  3QYG A;  2ZPH A;  2ZPG A;  4ZGD A;  3VYH A;  3A8M A;  3QXE A;  2CZ0 A;  3X25 A;  2ZCF A;  1UGQ A;  3X20 A;  1IRE A;  4OB3 A;  3WVE A;  2CZ7 A;  2ZPB A;  3A8H A;  2DD4 C;  2ZPI A;  2CYZ A;  2QDY A;  2ZZD C;  3A8O A;  2DD5 C;  2DXB C;  3HHT A;  4FM4 A;  2CZ6 A;  2DXC C;  3X28 A;  2D0Q A;  4OB2 A;  3QZ9 A;  2DPP 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...

2QDYA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations