1COV | Genus

Total Genus 3

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	3
sequence length	68
structure length	55
Chain Sequence	GAQVSTQKTGIHYTNINYYKDAASNSANRQDFTQDPSKFTEPVKDIMIKSLPALN

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__033754065379968__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__033754065379968__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1COV/4/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__033754065379968__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"033754065379968","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1COV/4/"

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__033754065379968__ ready

script 1 started

platformSpeed = 8

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
publication title	Structure determination of coxsackievirus B3 to 3.5 A resolution. pubmed doi rcsb
molecule keywords	COXSACKIEVIRUS COAT PROTEIN
total genus	3
structure length	55
sequence length	68
ec nomenclature	ec 2.7.7.48: RNA-directed RNA polymerase.
pdb deposition date	1994-10-19

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
4	PF02226	Pico_P1A	Picornavirus coat protein (VP4)

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

cath code	Class	Architecture	Topology	Homology	Domain
4.10.80.10	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	Picornavirus coat protein VP4	1cov400

1POV0 2PLV4 2RS54 4Q4V4 2RS14 1RMU4 2RS34 1PIV4 1R084 1NA1D 4PDWD 1EV14 1AL24 1AR74 1VBC4 1RUI4 1EAH4 1H8TD 1ASJ4 1RHI4 1AR94 1RVF4 2RMU4 2HWC4 1HXS4 3JBG4 1VRH4 1BEV4 4RHV4 1RUD4 1K5MD 1RUG4 1HRI4 1VBA4 4Q4W4 1RUJ4 3JD74 1COV4 3J8F4 1R094 2HWB4 1MQTD 2R064 4Q4Y4 2RR14 2R044 1VBD4 1NCQD 2RM24 1HRV4 2X5ID 1RUE4 1PO14 1VBE4 4GB34 1PO24 1AR84 1RUC4 1RUH4 1RUF4 2R074 1OOPD 1VBB4 1Z7S4 1PVC4 4Q4X4 1D4M4 1AR64
chains in the Genus database with same CATH superfamily

2PLV4 3AEAA 1KF6A 2WDQA 3AE7A 4Q4V4 3AEEA 5C3JA 1RMU4 3AE2A 1L0VA 2R7FA 1YQ3A 1EV14 2H88A 1NEKA 1VBC4 1RUI4 1EAH4 3SFDA 2PYJA 2WS3A 2HWC4 1KFYA 1K5MD 3AEGA 2WDVA 1VBD4 3VR8A 1NCQD 2X5ID 1RUE4 4GB34 1VBE4 1RUC4 1OOPD 1Z7S4 3P4QA 1PVC4 1D4M4 1YQ4A 1AR64 2RS14 1NA1D 3CIRA 1AL24 3AE8A 1ASJ4 1AR94 3FI7A 1HXS4 3AE1A 4YXDA 1RUD4 4Q4W4 3AEFA 4Q4Y4 2RR14 3VR9A 4YTPA 2R044 4KX6A 2RM24 1HRV4 4YSYA 3AE3A 3VRAA 2PY5A 2PYLA 1RUH4 2WP9A 1ZOYA 1XHZA 2RS34 1PIV4 3SUCA 2B76A 2PW9A 1RHI4 1ZP0A 3P4RA 2RMU4 3JBG4 4YSZA 1BEV4 1RUG4 3P4SA 3J8F4 2HWB4 2R064 1MQTD 3AEBA 1NENA 3AECA 3GQHA 1PO24 3AE5A 3AE4A 1RUF4 3AEDA 4YT0A 1POV0 3AE9A 2RS54 3VRBA 1XHXA 1R084 4PDWD 1AR74 1H8TD 2PZSA 1RVF4 4YTMA 4YTNA 1VRH4 3SFEA 4YSXA 2H89A 3AE6A 4RHV4 1HRI4 1VBA4 1RUJ4 3JD74 1COV4 1R094 2WU5A 2WQYA 2ACZA 2FBWA 1PO14 1XI1A 3P4PA 1AR84 3GQKA 2R074 1VBB4 2WDRA 3ABVA 2EX3A 4Q4X4 5C2TA 2WU2A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1POV 0;  2PLV 4;  2RS5 4;  4Q4V 4;  2RS1 4;  1RMU 4;  2RS3 4;  1PIV 4;  1R08 4;  1NA1 D;  4PDW D;  1EV1 4;  1AL2 4;  1AR7 4;  1VBC 4;  1RUI 4;  1EAH 4;  1H8T D;  1ASJ 4;  1RHI 4;  1AR9 4;  1RVF 4;  2RMU 4;  2HWC 4;  1HXS 4;  3JBG 4;  1VRH 4;  1BEV 4;  4RHV 4;  1RUD 4;  1K5M D;  1RUG 4;  1HRI 4;  1VBA 4;  4Q4W 4;  1RUJ 4;  3JD7 4;  1COV 4;  3J8F 4;  1R09 4;  2HWB 4;  1MQT D;  2R06 4;  4Q4Y 4;  2RR1 4;  2R04 4;  1VBD 4;  1NCQ D;  2RM2 4;  1HRV 4;  2X5I D;  1RUE 4;  1PO1 4;  1VBE 4;  4GB3 4;  1PO2 4;  1AR8 4;  1RUC 4;  1RUH 4;  1RUF 4;  2R07 4;  1OOP D;  1VBB 4;  1Z7S 4;  1PVC 4;  4Q4X 4;  1D4M 4;  1AR6 4; 
#chains in the Genus database with same CATH topology
 2PLV 4;  3AEA A;  1KF6 A;  2WDQ A;  3AE7 A;  4Q4V 4;  3AEE A;  5C3J A;  1RMU 4;  3AE2 A;  1L0V A;  2R7F A;  1YQ3 A;  1EV1 4;  2H88 A;  1NEK A;  1VBC 4;  1RUI 4;  1EAH 4;  3SFD A;  2PYJ A;  2WS3 A;  2HWC 4;  1KFY A;  1K5M D;  3AEG A;  2WDV A;  1VBD 4;  3VR8 A;  1NCQ D;  2X5I D;  1RUE 4;  4GB3 4;  1VBE 4;  1RUC 4;  1OOP D;  1Z7S 4;  3P4Q A;  1PVC 4;  1D4M 4;  1YQ4 A;  1AR6 4;  2RS1 4;  1NA1 D;  3CIR A;  1AL2 4;  3AE8 A;  1ASJ 4;  1AR9 4;  3FI7 A;  1HXS 4;  3AE1 A;  4YXD A;  1RUD 4;  4Q4W 4;  3AEF A;  4Q4Y 4;  2RR1 4;  3VR9 A;  4YTP A;  2R04 4;  4KX6 A;  2RM2 4;  1HRV 4;  4YSY A;  3AE3 A;  3VRA A;  2PY5 A;  2PYL A;  1RUH 4;  2WP9 A;  1ZOY A;  1XHZ A;  2RS3 4;  1PIV 4;  3SUC A;  2B76 A;  2PW9 A;  1RHI 4;  1ZP0 A;  3P4R A;  2RMU 4;  3JBG 4;  4YSZ A;  1BEV 4;  1RUG 4;  3P4S A;  3J8F 4;  2HWB 4;  2R06 4;  1MQT D;  3AEB A;  1NEN A;  3AEC A;  3GQH A;  1PO2 4;  3AE5 A;  3AE4 A;  1RUF 4;  3AED A;  4YT0 A;  1POV 0;  3AE9 A;  2RS5 4;  3VRB A;  1XHX A;  1R08 4;  4PDW D;  1AR7 4;  1H8T D;  2PZS A;  1RVF 4;  4YTM A;  4YTN A;  1VRH 4;  3SFE A;  4YSX A;  2H89 A;  3AE6 A;  4RHV 4;  1HRI 4;  1VBA 4;  1RUJ 4;  3JD7 4;  1COV 4;  1R09 4;  2WU5 A;  2WQY A;  2ACZ A;  2FBW A;  1PO1 4;  1XI1 A;  3P4P A;  1AR8 4;  3GQK A;  2R07 4;  1VBB 4;  2WDR A;  3ABV A;  2EX3 A;  4Q4X 4;  5C2T A;  2WU2 A; 
#chains in the Genus database with same CATH homology
 1POV 0;  2PLV 4;  2RS5 4;  4Q4V 4;  2RS1 4;  1RMU 4;  2RS3 4;  1PIV 4;  1R08 4;  1NA1 D;  4PDW D;  1EV1 4;  1AL2 4;  1AR7 4;  1VBC 4;  1RUI 4;  1EAH 4;  1H8T D;  1ASJ 4;  1RHI 4;  1AR9 4;  1RVF 4;  2RMU 4;  2HWC 4;  1HXS 4;  3JBG 4;  1VRH 4;  1BEV 4;  4RHV 4;  1RUD 4;  1K5M D;  1RUG 4;  1HRI 4;  1VBA 4;  4Q4W 4;  1RUJ 4;  3JD7 4;  1COV 4;  3J8F 4;  1R09 4;  2HWB 4;  1MQT D;  2R06 4;  4Q4Y 4;  2RR1 4;  2R04 4;  1VBD 4;  1NCQ D;  2RM2 4;  1HRV 4;  2X5I D;  1RUE 4;  1PO1 4;  1VBE 4;  4GB3 4;  1PO2 4;  1AR8 4;  1RUC 4;  1RUH 4;  1RUF 4;  2R07 4;  1OOP D;  1VBB 4;  1Z7S 4;  1PVC 4;  4Q4X 4;  1D4M 4;  1AR6 4;

...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...

1COV4

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations