2EB6 | Genus

Total Genus 85

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	85
sequence length	267
structure length	267
Chain Sequence	MFDKHTHTLIAQRLDQAEKQREQIRAISLDYPEITIEDAYAVQREWVRLKIAEGRTLKGHKIGLTSKAMQASSQISEPDYGALLDDMFFHDGSDIPTDRFIVPRIEVELAFVLAKPLRGPNCTLFDVYNATDYVIPALELIDARCHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKPDELDLRWISALMYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSFTRPVPARKGDTFHVDYGNMGSISCRFV

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__0349797186250753__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__0349797186250753__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2EB6/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__0349797186250753__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"0349797186250753","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2EB6/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__0349797186250753__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfce271602b290cf3167124/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfce271602b290cf3167124/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfce271602b290cf3167124/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/5cfce271602b290cf3167124/pdb.gz): 1010 ms

reading 267 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

267 atoms created

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

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:266});backbone only;select *;

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
source organism	Escherichia coli
publication title	Structure and Mechanism of HpcG, a Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia coli pubmed doi rcsb
molecule keywords	2-oxo-hept-3-ene-1,7-dioate hydratase
total genus	85
structure length	267
sequence length	267
chains with identical sequence	B, C, D, E
ec nomenclature	ec 4.2.1.-:
pdb deposition date	2007-02-07

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01557	FAA_hydrolase	Fumarylacetoacetate (FAA) hydrolase family

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

cath code	Class	Architecture	Topology	Homology	Domain
3.90.850.10	Alpha Beta	Alpha-Beta Complex	Fumarylacetoacetate hydrolase; domain 2	Fumarylacetoacetase-like, C-terminal domain	2eb6A00

3QDFA 3RR6A 1HYOA 2HZYA 2Q1CX 1QCNA 5D2GA 4QKUA 1SAWA 5D2FA 2Q1DX 2DFUA 1SV6A 1NR9A 1GTTA 2Q18X 1QQJA 2Q19X 2WQTA 2EB6A 1I7OA 4DBHA 3S52A 1QCOA 2Q1AX 1NKQA 5D2IA 5D2HA 2EB4A 4MAQA 1WZOA 5D2KA 2EB5A 3V77A 3LZKA 3R6OA 3BQBA 4PFZA 4DBFA 5D2JA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 3QDF A;  3RR6 A;  1HYO A;  2HZY A;  2Q1C X;  1QCN A;  5D2G A;  4QKU A;  1SAW A;  5D2F A;  2Q1D X;  2DFU A;  1SV6 A;  1NR9 A;  1GTT A;  2Q18 X;  1QQJ A;  2Q19 X;  2WQT A;  2EB6 A;  1I7O A;  4DBH A;  3S52 A;  1QCO A;  2Q1A X;  1NKQ A;  5D2I A;  5D2H A;  2EB4 A;  4MAQ A;  1WZO A;  5D2K A;  2EB5 A;  3V77 A;  3LZK A;  3R6O A;  3BQB A;  4PFZ A;  4DBF A;  5D2J A; 
#chains in the Genus database with same CATH topology
 3QDF A;  3RR6 A;  1HYO A;  2HZY A;  2Q1C X;  1QCN A;  5D2G A;  4QKU A;  1SAW A;  5D2F A;  2Q1D X;  2DFU A;  1SV6 A;  1NR9 A;  1GTT A;  2Q18 X;  1QQJ A;  2Q19 X;  2WQT A;  2EB6 A;  1I7O A;  4DBH A;  3S52 A;  1QCO A;  2Q1A X;  1NKQ A;  5D2I A;  5D2H A;  2EB4 A;  4MAQ A;  1WZO A;  5D2K A;  2EB5 A;  3V77 A;  3LZK A;  3R6O A;  3BQB A;  4PFZ A;  4DBF A;  5D2J A; 
#chains in the Genus database with same CATH homology
 3QDF A;  3RR6 A;  1HYO A;  2HZY A;  2Q1C X;  1QCN A;  5D2G A;  4QKU A;  1SAW A;  5D2F A;  2Q1D X;  2DFU A;  1SV6 A;  1NR9 A;  1GTT A;  2Q18 X;  1QQJ A;  2Q19 X;  2WQT A;  2EB6 A;  1I7O A;  4DBH A;  3S52 A;  1QCO A;  2Q1A X;  1NKQ A;  5D2I A;  5D2H A;  2EB4 A;  4MAQ A;  1WZO A;  5D2K A;  2EB5 A;  3V77 A;  3LZK A;  3R6O A;  3BQB A;  4PFZ A;  4DBF A;  5D2J 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...

2EB6A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations