4QP5 | Genus

Total Genus 32

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	32
sequence length	134
structure length	134
Chain Sequence	HEHSAQWLNNYKKGYGYGPYPLGINGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGGNQIGLIENDGVHRQWYMHLSKYNVKVGDYVKAGQIIGWSGSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKS

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__34360353403006__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__34360353403006__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4QP5/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__34360353403006__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"34360353403006","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4QP5/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__34360353403006__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d009cd777b9c70ac1b03491/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d009cd777b9c70ac1b03491/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d009cd777b9c70ac1b03491/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/5d009cd777b9c70ac1b03491/pdb.gz): 255 ms

reading 134 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

134 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:133});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

molecule tags	Hydrolase
source organism	Staphylococcus simulans bv. staphylolyticus
publication title	Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans. pubmed doi rcsb
molecule keywords	Lysostaphin
total genus	32
structure length	134
sequence length	134
chains with identical sequence	B
ec nomenclature	ec 3.4.24.75: Lysostaphin.
pdb deposition date	2014-06-22

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01551	Peptidase_M23	Peptidase family M23

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

cath code	Class	Architecture	Topology	Homology	Domain
2.70.70.10	Mainly Beta	Distorted Sandwich	Glucose Permease (Domain IIA)	Glucose Permease (Domain IIA)	4qp5A00

3CSQA 3UZ0B 3IT7A 4QPBA 4LXCA 1O2FA 3SLUA 2MP0B 1GLAF 1GGRA 2B13A 5KVPA 5B0HA 1GPRA 1GLDF 2GU1A 4ZYBA 2GPRA 2F3GA 1QWYA 4BH5A 4RNYA 1F3ZA 2B44A 3TUFB 1GLEF 1GLCF 4JBWM 3NYYA 1AX3A 2B0PA 3IT5A 1F3GA 2HSIA 4RNZA 1GLBF 4QP5A 3OURB
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 3CSQ A;  3UZ0 B;  3IT7 A;  4QPB A;  4LXC A;  1O2F A;  3SLU A;  2MP0 B;  1GLA F;  1GGR A;  2B13 A;  5KVP A;  5B0H A;  1GPR A;  1GLD F;  2GU1 A;  4ZYB A;  2GPR A;  2F3G A;  1QWY A;  4BH5 A;  4RNY A;  1F3Z A;  2B44 A;  3TUF B;  1GLE F;  1GLC F;  4JBW M;  3NYY A;  1AX3 A;  2B0P A;  3IT5 A;  1F3G A;  2HSI A;  4RNZ A;  1GLB F;  4QP5 A;  3OUR B; 
#chains in the Genus database with same CATH topology
 3CSQ A;  3UZ0 B;  3IT7 A;  4QPB A;  4LXC A;  1O2F A;  3SLU A;  2MP0 B;  1GLA F;  1GGR A;  2B13 A;  5KVP A;  5B0H A;  1GPR A;  1GLD F;  2GU1 A;  4ZYB A;  2GPR A;  2F3G A;  1QWY A;  4BH5 A;  4RNY A;  1F3Z A;  2B44 A;  3TUF B;  1GLE F;  1GLC F;  4JBW M;  3NYY A;  1AX3 A;  2B0P A;  3IT5 A;  1F3G A;  2HSI A;  4RNZ A;  1GLB F;  4QP5 A;  3OUR B; 
#chains in the Genus database with same CATH homology
 3CSQ A;  3UZ0 B;  3IT7 A;  4QPB A;  4LXC A;  1O2F A;  3SLU A;  2MP0 B;  1GLA F;  1GGR A;  2B13 A;  5KVP A;  5B0H A;  1GPR A;  1GLD F;  2GU1 A;  4ZYB A;  2GPR A;  2F3G A;  1QWY A;  4BH5 A;  4RNY A;  1F3Z A;  2B44 A;  3TUF B;  1GLE F;  1GLC F;  4JBW M;  3NYY A;  1AX3 A;  2B0P A;  3IT5 A;  1F3G A;  2HSI A;  4RNZ A;  1GLB F;  4QP5 A;  3OUR B;

...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...

4QP5A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations