1KMD | Genus

Total Genus 17

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	17
sequence length	117
structure length	117
Chain Sequence	KMSEKLRIKVDDVKINPKYVLYGVSTPNKRLYKRYSEFWKLKTRLERDVGSTIPYDFPEKPGVLDRRWQRRYDDPEMIDERRIGLERFLNELYNDRFDSRWRDTKIAQDFLQLSKPN

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__7717173824684718__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__7717173824684718__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1KMD/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__7717173824684718__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"7717173824684718","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1KMD/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__7717173824684718__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d29acacc7644b0c19bd7d09/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d29acacc7644b0c19bd7d09/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d29acacc7644b0c19bd7d09/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/5d29acacc7644b0c19bd7d09/pdb.gz): 457 ms

reading 117 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

117 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:116});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	Endocytosis/exocytosis
source organism	Saccharomyces cerevisiae
publication title	Solution structure of the Vam7p PX domain. pubmed doi rcsb
molecule keywords	Vacuolar morphogenesis protein VAM7
total genus	17
structure length	117
sequence length	117
ec nomenclature
pdb deposition date	2001-12-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00787	PX	PX domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	1kmdA00

4HASA 3HPBA 1H6HA 2REDA 1XTEA 1OCSA 4PZGA 4AZ9A 4IKBB 2RAKA 2L73A 3HPCX 1OCUA 2CZOA 2V14A 2YPSA 2WWEA 2V6VA 4PQPA 4BGJA 1GD5A 4AKVA 1KMDA 4IKBA 3IQ2A 4IKDA 2I4KA 4PQOA 2AR5A 1O7KA 2ETTA 2REAA 2RAJA 3FOGA 3DYTA 2IWLX 1XTNA 2RAIA 3LUIA 2CSKA 3P0CA 4ON3A 4P2IA 4OXWA 1KQ6A 2DYBA 4P2JA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 4HAS A;  3HPB A;  1H6H A;  2RED A;  1XTE A;  1OCS A;  4PZG A;  4AZ9 A;  4IKB B;  2RAK A;  2L73 A;  3HPC X;  1OCU A;  2CZO A;  2V14 A;  2YPS A;  2WWE A;  2V6V A;  4PQP A;  4BGJ A;  1GD5 A;  4AKV A;  1KMD A;  4IKB A;  3IQ2 A;  4IKD A;  2I4K A;  4PQO A;  2AR5 A;  1O7K A;  2ETT A;  2REA A;  2RAJ A;  3FOG A;  3DYT A;  2IWL X;  1XTN A;  2RAI A;  3LUI A;  2CSK A;  3P0C A;  4ON3 A;  4P2I A;  4OXW A;  1KQ6 A;  2DYB A;  4P2J A; 
#chains in the Genus database with same CATH topology
 4HAS A;  3HPB A;  1H6H A;  2RED A;  1XTE A;  1OCS A;  4PZG A;  4AZ9 A;  4IKB B;  2RAK A;  2L73 A;  3HPC X;  1OCU A;  2CZO A;  2V14 A;  2YPS A;  2WWE A;  2V6V A;  4PQP A;  4BGJ A;  1GD5 A;  4AKV A;  1KMD A;  4IKB A;  3IQ2 A;  4IKD A;  2I4K A;  4PQO A;  2AR5 A;  1O7K A;  2ETT A;  2REA A;  2RAJ A;  3FOG A;  3DYT A;  2IWL X;  1XTN A;  2RAI A;  3LUI A;  2CSK A;  3P0C A;  4ON3 A;  4P2I A;  4OXW A;  1KQ6 A;  2DYB A;  4P2J A; 
#chains in the Genus database with same CATH homology
 4HAS A;  3HPB A;  1H6H A;  2RED A;  1XTE A;  1OCS A;  4PZG A;  4AZ9 A;  4IKB B;  2RAK A;  2L73 A;  3HPC X;  1OCU A;  2CZO A;  2V14 A;  2YPS A;  2WWE A;  2V6V A;  4PQP A;  4BGJ A;  1GD5 A;  4AKV A;  1KMD A;  4IKB A;  3IQ2 A;  4IKD A;  2I4K A;  4PQO A;  2AR5 A;  1O7K A;  2ETT A;  2REA A;  2RAJ A;  3FOG A;  3DYT A;  2IWL X;  1XTN A;  2RAI A;  3LUI A;  2CSK A;  3P0C A;  4ON3 A;  4P2I A;  4OXW A;  1KQ6 A;  2DYB A;  4P2J 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...

1KMDA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations