3VMQ | Genus

Total Genus 83

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	83
sequence length	229
structure length	223
Chain Sequence	RILLKILLTILIIIALFIGIMYFLSTRDNVDELRKIENKSSFVSADNMPEYVKGAFISMEDERFYNHHGFDLKGTTRALFSTQGGSTITQQVVKNYFYDNDRSFTRKVKELFVAHRVEKQYNKNEILSFYLNNIYFGDNQYTLEGAANHYFGTTVNKNSTTMSHITVLQSAILASKVNAPSVYNINNMSENFTQRVSTNLEKMKQQNYINETQYQQAMSQLNR

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__5800699860466825__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__5800699860466825__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3VMQ/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__5800699860466825__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"5800699860466825","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3VMQ/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__5800699860466825__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d03593a6b155ddeeec93d22/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d03593a6b155ddeeec93d22/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d03593a6b155ddeeec93d22/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/5d03593a6b155ddeeec93d22/pdb.gz): 446 ms

reading 223 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

223 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:222});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	Transferase
source organism	Staphylococcus aureus
publication title	Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism pubmed doi rcsb
molecule keywords	Monofunctional glycosyltransferase
total genus	83
structure length	223
sequence length	229
chains with identical sequence	B
ec nomenclature	ec 2.4.1.129: Peptidoglycan glycosyltransferase.
pdb deposition date	2011-12-15

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00912	Transgly	Transglycosylase

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.3810.10	Mainly Alpha	Orthogonal Bundle	Penicillin binding protein transpeptidase fold	Biosynthetic peptidoglycan transglycosylase-like	3vmqA00

3D3HA 3DWKA 3NB7A 3VMAA 2OLVA 2OQOA 3VMSA 3VMRA 3NB6A 3VMQA 3FWLA 3HZSA 3ZG7B 3VMTA 2OLUA
chains in the Genus database with same CATH superfamily

3D3HA 3DWKA 3NB7A 3VMAA 2OLVA 2OQOA 3VMSA 3VMRA 3NB6A 3VMQA 3FWLA 3HZSA 3ZG7B 3VMTA 2OLUA
chains in the Genus database with same CATH topology

3D3HA 3DWKA 3NB7A 3VMAA 2OLVA 2OQOA 3VMSA 3VMRA 3NB6A 3VMQA 3FWLA 3HZSA 3ZG7B 3VMTA 2OLUA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3D3H A;  3DWK A;  3NB7 A;  3VMA A;  2OLV A;  2OQO A;  3VMS A;  3VMR A;  3NB6 A;  3VMQ A;  3FWL A;  3HZS A;  3ZG7 B;  3VMT A;  2OLU A; 
#chains in the Genus database with same CATH topology
 3D3H A;  3DWK A;  3NB7 A;  3VMA A;  2OLV A;  2OQO A;  3VMS A;  3VMR A;  3NB6 A;  3VMQ A;  3FWL A;  3HZS A;  3ZG7 B;  3VMT A;  2OLU A; 
#chains in the Genus database with same CATH homology
 3D3H A;  3DWK A;  3NB7 A;  3VMA A;  2OLV A;  2OQO A;  3VMS A;  3VMR A;  3NB6 A;  3VMQ A;  3FWL A;  3HZS A;  3ZG7 B;  3VMT A;  2OLU 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...

3VMQA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations