5KH2 | Genus

Total Genus 84

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	84
sequence length	229
structure length	224
Chain Sequence	QVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFSRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNRRH

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__3464902982742055__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__3464902982742055__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/5KH2/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__3464902982742055__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3464902982742055","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/5KH2/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__3464902982742055__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0e39a3e830ce68657cae09/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0e39a3e830ce68657cae09/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0e39a3e830ce68657cae09/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/5d0e39a3e830ce68657cae09/pdb.gz): 396 ms

reading 224 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

224 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:223});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	Discovery and Characterization of a Class of Pyrazole Inhibitors of Bacterial Undecaprenyl Pyrophosphate Synthase. pubmed doi rcsb
molecule keywords	Isoprenyl transferase
molecule tags	Transferase
source organism	Streptococcus pneumoniae serotype 4 (strain atcc baa-334 / tigr4)
total genus	84
structure length	224
sequence length	229
chains with identical sequence	B, C, D
ec nomenclature	ec 2.5.1.-:
pdb deposition date	2016-06-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01255	Prenyltransf	Putative undecaprenyl diphosphate synthase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.1180.10	Alpha Beta	3-Layer(aba) Sandwich	Undecaprenyl pyrophosphate synthetase	Decaprenyl diphosphate synthase-like	5kh2A00

2D2RA 4H3AA 1X08A 4H2OA 1X09A 1F75A 1V7UA 2VG3A 4CMWA 2E9AA 2E98A 3QASA 3TH8A 3WYIA 5HXTA 3SGVA 4Q9MA 2VG4A 5HXQA 5KH4A 2VG0A 5HXPA 2E9CA 1JP3A 4KT8A 5CQJA 4CMVA 5HXOA 3WYJA 2VFWA 4H3CA 3UGSA 5HC8A 5CQBA 5KH5A 3SGTA 1UEHA 4ONCA 2E9DA 2VG2A 4CMXA 3WQLA 2VG1A 2DTNA 4H2MA 4H38A 3SGXA 3WQMA 5KH2A 5HC6A 1X07A 4Q9OA 3WQNA 4H2JA 5HXNA 1X06A 5HC7A 4H8EA 3SH0A 3WQKA 4U82A 2E99A
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2D2R A;  4H3A A;  1X08 A;  4H2O A;  1X09 A;  1F75 A;  1V7U A;  2VG3 A;  4CMW A;  2E9A A;  2E98 A;  3QAS A;  3TH8 A;  3WYI A;  5HXT A;  3SGV A;  4Q9M A;  2VG4 A;  5HXQ A;  5KH4 A;  2VG0 A;  5HXP A;  2E9C A;  1JP3 A;  4KT8 A;  5CQJ A;  4CMV A;  5HXO A;  3WYJ A;  2VFW A;  4H3C A;  3UGS A;  5HC8 A;  5CQB A;  5KH5 A;  3SGT A;  1UEH A;  4ONC A;  2E9D A;  2VG2 A;  4CMX A;  3WQL A;  2VG1 A;  2DTN A;  4H2M A;  4H38 A;  3SGX A;  3WQM A;  5KH2 A;  5HC6 A;  1X07 A;  4Q9O A;  3WQN A;  4H2J A;  5HXN A;  1X06 A;  5HC7 A;  4H8E A;  3SH0 A;  3WQK A;  4U82 A;  2E99 A; 
#chains in the Genus database with same CATH topology
 2D2R A;  4H3A A;  1X08 A;  4H2O A;  1X09 A;  1F75 A;  1V7U A;  2VG3 A;  4CMW A;  2E9A A;  2E98 A;  3QAS A;  3TH8 A;  3WYI A;  5HXT A;  3SGV A;  4Q9M A;  2VG4 A;  5HXQ A;  5KH4 A;  2VG0 A;  5HXP A;  2E9C A;  1JP3 A;  4KT8 A;  5CQJ A;  4CMV A;  5HXO A;  3WYJ A;  2VFW A;  4H3C A;  3UGS A;  5HC8 A;  5CQB A;  5KH5 A;  3SGT A;  1UEH A;  4ONC A;  2E9D A;  2VG2 A;  4CMX A;  3WQL A;  2VG1 A;  2DTN A;  4H2M A;  4H38 A;  3SGX A;  3WQM A;  5KH2 A;  5HC6 A;  1X07 A;  4Q9O A;  3WQN A;  4H2J A;  5HXN A;  1X06 A;  5HC7 A;  4H8E A;  3SH0 A;  3WQK A;  4U82 A;  2E99 A; 
#chains in the Genus database with same CATH homology
 2D2R A;  4H3A A;  1X08 A;  4H2O A;  1X09 A;  1F75 A;  1V7U A;  2VG3 A;  4CMW A;  2E9A A;  2E98 A;  3QAS A;  3TH8 A;  3WYI A;  5HXT A;  3SGV A;  4Q9M A;  2VG4 A;  5HXQ A;  5KH4 A;  2VG0 A;  5HXP A;  2E9C A;  1JP3 A;  4KT8 A;  5CQJ A;  4CMV A;  5HXO A;  3WYJ A;  2VFW A;  4H3C A;  3UGS A;  5HC8 A;  5CQB A;  5KH5 A;  3SGT A;  1UEH A;  4ONC A;  2E9D A;  2VG2 A;  4CMX A;  3WQL A;  2VG1 A;  2DTN A;  4H2M A;  4H38 A;  3SGX A;  3WQM A;  5KH2 A;  5HC6 A;  1X07 A;  4Q9O A;  3WQN A;  4H2J A;  5HXN A;  1X06 A;  5HC7 A;  4H8E A;  3SH0 A;  3WQK A;  4U82 A;  2E99 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...

5KH2A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations