2HLD | Genus

Total Genus 19

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	19
sequence length	126
structure length	120
Chain Sequence	KLQFALPHETLYSEVTQVNLPAKSGRIGVLANHVPTVEQLLPGVVEVMEGSNSKKFFISGGFATVQPDSQLCVTAIEAPLESFSENIKNLLAEAKKNVSSSREAAEAAIQVEVLENLQSV

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__468538023593339__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__468538023593339__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2HLD/H/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__468538023593339__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"468538023593339","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2HLD/H/"

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__468538023593339__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd242a79a9a72ad1456b80/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd242a79a9a72ad1456b80/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd242a79a9a72ad1456b80/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/5cfd242a79a9a72ad1456b80/pdb.gz): 804 ms

reading 120 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

120 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:119});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

publication title	Novel features of the rotary catalytic mechanism revealed in the structure of yeast F(1) ATPase. pubmed doi rcsb
molecule keywords	ATP synthase alpha chain, mitochondrial
molecule tags	Hydrolase
source organism	Saccharomyces cerevisiae
total genus	19
structure length	120
sequence length	126
chains with identical sequence	Q, Z
ec nomenclature
pdb deposition date	2006-07-06

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
H	PF02823	ATP-synt_DE_N	ATP synthase, Delta/Epsilon chain, beta-sandwich domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.15.10	Mainly Beta	Sandwich	ATP Synthase; domain 1	F0F1 ATP synthase delta/epsilon subunit, N-terminal	2hldH01

4ASUH 1BSNA 3FKSH 2XNDH 1FS0E 2E5YA 3OFNH 2HLDH 5DN6I 3OEHH 2V7QH 5FL7H 2WSSH 2QE7H 4YXWH 1AQTA 3OAAH 2RQ7A 1H8EH 3OE7H 1BSHA 1E79H 2RQ6A 2XOKH
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 4ASU H;  1BSN A;  3FKS H;  2XND H;  1FS0 E;  2E5Y A;  3OFN H;  2HLD H;  5DN6 I;  3OEH H;  2V7Q H;  5FL7 H;  2WSS H;  2QE7 H;  4YXW H;  1AQT A;  3OAA H;  2RQ7 A;  1H8E H;  3OE7 H;  1BSH A;  1E79 H;  2RQ6 A;  2XOK H; 
#chains in the Genus database with same CATH topology
 4ASU H;  1BSN A;  3FKS H;  2XND H;  1FS0 E;  2E5Y A;  3OFN H;  2HLD H;  5DN6 I;  3OEH H;  2V7Q H;  5FL7 H;  2WSS H;  2QE7 H;  4YXW H;  1AQT A;  3OAA H;  2RQ7 A;  1H8E H;  3OE7 H;  1BSH A;  1E79 H;  2RQ6 A;  2XOK H; 
#chains in the Genus database with same CATH homology
 4ASU H;  1BSN A;  3FKS H;  2XND H;  1FS0 E;  2E5Y A;  3OFN H;  2HLD H;  5DN6 I;  3OEH H;  2V7Q H;  5FL7 H;  2WSS H;  2QE7 H;  4YXW H;  1AQT A;  3OAA H;  2RQ7 A;  1H8E H;  3OE7 H;  1BSH A;  1E79 H;  2RQ6 A;  2XOK H;

...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...

2HLDH

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations