1H2C | Genus

Total Genus 22

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	22
sequence length	124
structure length	124
Chain Sequence	VSSAFILEAMVNVISGPKVLMKQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKATNPLVRVNRLGPGIPDHPLRLLRIGNQAFLQEFVLPPVQLPQYFTFDLTALKLITQPLPAATWT

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__4099235512425503__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__4099235512425503__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1h2c/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__4099235512425503__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"4099235512425503","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1h2c/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__4099235512425503__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d2683748e26e1f261c5ce5d/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d2683748e26e1f261c5ce5d/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d2683748e26e1f261c5ce5d/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/5d2683748e26e1f261c5ce5d/pdb.gz): 1116 ms

reading 124 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

124 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:123});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	Virus/viral protein
source organism	Ebola virus
publication title	The Matrix Protein Vp40 from Ebola Virus Octamerizes Into Pore-Like Structures with Specific RNA Binding Properties pubmed doi rcsb
molecule keywords	MATRIX PROTEIN VP40
total genus	22
structure length	124
sequence length	124
ec nomenclature
pdb deposition date	2002-08-05

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

cath code	Class	Architecture	Topology	Homology	Domain
2.70.20.20	Mainly Beta	Distorted Sandwich	Topoisomerase I; domain 3	Topoisomerase I; domain 3	1h2cA00

1H2DA 3TCQA 4LD8A 1ES6A 4LDBA 1H2CA 4LDDA 5B0VA 4LDMA
chains in the Genus database with same CATH superfamily

4HI5A 1I7DA 1CY7A 3PWTA 1MW9X 3TCQA 1CY6A 2O19A 4CHTA 1CY0A 2VQPA 4HITA 4LDDA 4D4TA 1CY4A 2YKDA 2GAIA 4HI6A 4LDBA 4CGYA 1MW8X 4G1GA 5D5HA 2O59A 2O54A 4RULA 4HIYA 4LD8A 2O5CA 1H2CA 1CY1A 1CYYA 4V23A 5B0VA 4LDMA 3PX7A 1H2DA 4LP7A 2O5EA 1CY8A 1CY2A 4HIUA 4HIWA 1ES6A 2GAJA 1CY9A 1ECLA 4G1OA 3F1JA 1D6MA 4G1LA
chains in the Genus database with same CATH topology

4HI5A 3TCQA 2VQPA 4HITA 4LDDA 4D4TA 2YKDA 4HI6A 4LDBA 4G1LA 4G1GA 4HIYA 4LD8A 1H2CA 4V23A 5B0VA 4LDMA 1H2DA 4HIUA 4HIWA 1ES6A 4G1OA 3F1JA 4LP7A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 1H2D A;  3TCQ A;  4LD8 A;  1ES6 A;  4LDB A;  1H2C A;  4LDD A;  5B0V A;  4LDM A; 
#chains in the Genus database with same CATH topology
 4HI5 A;  1I7D A;  1CY7 A;  3PWT A;  1MW9 X;  3TCQ A;  1CY6 A;  2O19 A;  4CHT A;  1CY0 A;  2VQP A;  4HIT A;  4LDD A;  4D4T A;  1CY4 A;  2YKD A;  2GAI A;  4HI6 A;  4LDB A;  4CGY A;  1MW8 X;  4G1G A;  5D5H A;  2O59 A;  2O54 A;  4RUL A;  4HIY A;  4LD8 A;  2O5C A;  1H2C A;  1CY1 A;  1CYY A;  4V23 A;  5B0V A;  4LDM A;  3PX7 A;  1H2D A;  4LP7 A;  2O5E A;  1CY8 A;  1CY2 A;  4HIU A;  4HIW A;  1ES6 A;  2GAJ A;  1CY9 A;  1ECL A;  4G1O A;  3F1J A;  1D6M A;  4G1L A; 
#chains in the Genus database with same CATH homology
 4HI5 A;  3TCQ A;  2VQP A;  4HIT A;  4LDD A;  4D4T A;  2YKD A;  4HI6 A;  4LDB A;  4G1L A;  4G1G A;  4HIY A;  4LD8 A;  1H2C A;  4V23 A;  5B0V A;  4LDM A;  1H2D A;  4HIU A;  4HIW A;  1ES6 A;  4G1O A;  3F1J A;  4LP7 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...

1H2CA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN