3HQF | Genus

Total Genus 49

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	49
sequence length	173
structure length	173
Chain Sequence	HHGSSVFHNWLLEIACENYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYYNSRHFGKTRNEKRITRWGRGSPLQDPENTGALTLLAFKLDEQGGDCKEVNIWVCASTDEEDVIETAIGEVIPGALISGPAGQILGGL

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__333767668748898__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__333767668748898__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3HQF/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__333767668748898__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"333767668748898","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3HQF/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__333767668748898__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d17f6d093a465de6758cdd3/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d17f6d093a465de6758cdd3/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d17f6d093a465de6758cdd3/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/5d17f6d093a465de6758cdd3/pdb.gz): 470 ms

reading 173 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

173 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:172});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	Hydrolase/dna
source organism	Escherichia coli
publication title	Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. pubmed doi rcsb
molecule keywords	Restriction endonuclease
total genus	49
structure length	173
sequence length	173
ec nomenclature	ec 3.1.21.4: Type II site-specific deoxyribonuclease.
pdb deposition date	2009-06-06

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF09217	EcoRII-N	Restriction endonuclease EcoRII, N-terminal

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

cath code	Class	Architecture	Topology	Homology	Domain
2.40.330.10	Mainly Beta	Beta Barrel	At1g16640 B3 domain	DNA-binding pseudobarrel domain	3hqfA00

1NA6A 1YELA 4LDUA 4LDXA 1WIDA 4I1KA 3HQFA 4LDVA 4LDYA 4LDWA
chains in the Genus database with same CATH superfamily

3ZI5A 2C1LA 1NA6A 1N0GA 1N0EA 1YELA 4LDUA 4LDXA 1N0FA 1WIDA 4I1KA 3HQFA 4LDVA 4LDYA 4LDWA
chains in the Genus database with same CATH topology

1NA6A 1YELA 4LDUA 4LDXA 1WIDA 4I1KA 3HQFA 4LDVA 4LDYA 4LDWA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 1NA6 A;  1YEL A;  4LDU A;  4LDX A;  1WID A;  4I1K A;  3HQF A;  4LDV A;  4LDY A;  4LDW A; 
#chains in the Genus database with same CATH topology
 3ZI5 A;  2C1L A;  1NA6 A;  1N0G A;  1N0E A;  1YEL A;  4LDU A;  4LDX A;  1N0F A;  1WID A;  4I1K A;  3HQF A;  4LDV A;  4LDY A;  4LDW A; 
#chains in the Genus database with same CATH homology
 1NA6 A;  1YEL A;  4LDU A;  4LDX A;  1WID A;  4I1K A;  3HQF A;  4LDV A;  4LDY A;  4LDW 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...

3HQFA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations