5JNE | Genus

Total Genus 51

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	51
sequence length	254
structure length	254
Chain Sequence	MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSDILREGNNTDTLTLIADNTPDSIILLFEDTKKDDIAEYSLKLMDIDADFLGIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITCETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKF

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__7518199571284154__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__7518199571284154__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/5JNE/D/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__7518199571284154__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"7518199571284154","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/5JNE/D/"

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__7518199571284154__ 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	Ligase/signaling protein
source organism	Saccharomyces cerevisiae
publication title	Capturing a substrate in an activated RING E3/E2-SUMO complex. pubmed doi rcsb
molecule keywords	E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3
total genus	51
structure length	254
sequence length	254
chains with identical sequence	H
ec nomenclature
pdb deposition date	2016-04-29

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
D	PF00705	PCNA_N	Proliferating cell nuclear antigen, N-terminal domain
D	PF02747	PCNA_C	Proliferating cell nuclear antigen, C-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen	Proliferating Cell Nuclear Antigen	5jneD00

3A1JB 1W60A 4L60A 3U5ZF 3P87A 3P91A 5DA7A 2IZOB 2IO4A 3LX2A 1U76A 3U60F 1RXZA 2HIKB 2IX2C 3V60B 5B7OA 3F1WA 3G65B 1GE8A 4TR6A 3LX1A 3TBLA 2OD8A 2IJXA 4ZTDA 3U61F 1PLRA 3K4XA 2Z0LA 1UL1A 2ZVLA 1B77A 3HSLX 2IO4B 5E0TA 3A2FB 4L6PA 5JNED 1DMLA 3I2MX 2HIIA 1IZ5A 2HIIC 2ZVWA 2IX2A 5CFKA 1YYPA 1IZ4A 1RXMA 1CZDA 5IXAA 4RJFA 1PLQA 3P83A 5DAIA 5A6DA 1B8HA 2ZVVA 1U7BA 3V62B 3AIXA 1RWZA 3WGWA 4D2GA 2HIIB 3GGRA 3GGRC 1T6LA 2IX2B 3FDSD 5H0TA 2AVTA 1SXJF 3IFVA 2ZVMA 5IY4A 3AIZA 3AIZC 4CS5A 2NTIA 2NTIC 3A1JA 2AWAA 3A1JC 5E0UA 4YHRA 3V61B 1UD9A 5AUJA 5E0VA 3GPMA 3HI8A 1AXCA 2ZVKA 2IZOC 3AIXB 3GPNA 1VYMA 5HACA 5IWDA 1VYJA 3GGRB 2HIKA 2HIKC 3VKXA 3G65A 3FDSC 3G65C 1ISQA 4HK1A 2NTIB
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 3A1J B;  1W60 A;  4L60 A;  3U5Z F;  3P87 A;  3P91 A;  5DA7 A;  2IZO B;  2IO4 A;  3LX2 A;  1U76 A;  3U60 F;  1RXZ A;  2HIK B;  2IX2 C;  3V60 B;  5B7O A;  3F1W A;  3G65 B;  1GE8 A;  4TR6 A;  3LX1 A;  3TBL A;  2OD8 A;  2IJX A;  4ZTD A;  3U61 F;  1PLR A;  3K4X A;  2Z0L A;  1UL1 A;  2ZVL A;  1B77 A;  3HSL X;  2IO4 B;  5E0T A;  3A2F B;  4L6P A;  5JNE D;  1DML A;  3I2M X;  2HII A;  1IZ5 A;  2HII C;  2ZVW A;  2IX2 A;  5CFK A;  1YYP A;  1IZ4 A;  1RXM A;  1CZD A;  5IXA A;  4RJF A;  1PLQ A;  3P83 A;  5DAI A;  5A6D A;  1B8H A;  2ZVV A;  1U7B A;  3V62 B;  3AIX A;  1RWZ A;  3WGW A;  4D2G A;  2HII B;  3GGR A;  3GGR C;  1T6L A;  2IX2 B;  3FDS D;  5H0T A;  2AVT A;  1SXJ F;  3IFV A;  2ZVM A;  5IY4 A;  3AIZ A;  3AIZ C;  4CS5 A;  2NTI A;  2NTI C;  3A1J A;  2AWA A;  3A1J C;  5E0U A;  4YHR A;  3V61 B;  1UD9 A;  5AUJ A;  5E0V A;  3GPM A;  3HI8 A;  1AXC A;  2ZVK A;  2IZO C;  3AIX B;  3GPN A;  1VYM A;  5HAC A;  5IWD A;  1VYJ A;  3GGR B;  2HIK A;  2HIK C;  3VKX A;  3G65 A;  3FDS C;  3G65 C;  1ISQ A;  4HK1 A;  2NTI B; 
#chains in the Genus database with same CATH topology
 3A1J B;  1W60 A;  4L60 A;  3U5Z F;  3P87 A;  3P91 A;  5DA7 A;  2IZO B;  2IO4 A;  3LX2 A;  1U76 A;  3U60 F;  1RXZ A;  2HIK B;  2IX2 C;  3V60 B;  5B7O A;  3F1W A;  3G65 B;  1GE8 A;  4TR6 A;  3LX1 A;  3TBL A;  2OD8 A;  2IJX A;  4ZTD A;  3U61 F;  1PLR A;  3K4X A;  2Z0L A;  1UL1 A;  2ZVL A;  1B77 A;  3HSL X;  2IO4 B;  5E0T A;  3A2F B;  4L6P A;  5JNE D;  1DML A;  3I2M X;  2HII A;  1IZ5 A;  2HII C;  2ZVW A;  2IX2 A;  5CFK A;  1YYP A;  1IZ4 A;  1RXM A;  1CZD A;  5IXA A;  4RJF A;  1PLQ A;  3P83 A;  5DAI A;  5A6D A;  1B8H A;  2ZVV A;  1U7B A;  3V62 B;  3AIX A;  1RWZ A;  3WGW A;  4D2G A;  2HII B;  3GGR A;  3GGR C;  1T6L A;  2IX2 B;  3FDS D;  5H0T A;  2AVT A;  1SXJ F;  3IFV A;  2ZVM A;  5IY4 A;  3AIZ A;  3AIZ C;  4CS5 A;  2NTI A;  2NTI C;  3A1J A;  2AWA A;  3A1J C;  5E0U A;  4YHR A;  3V61 B;  1UD9 A;  5AUJ A;  5E0V A;  3GPM A;  3HI8 A;  1AXC A;  2ZVK A;  2IZO C;  3AIX B;  3GPN A;  1VYM A;  5HAC A;  5IWD A;  1VYJ A;  3GGR B;  2HIK A;  2HIK C;  3VKX A;  3G65 A;  3FDS C;  3G65 C;  1ISQ A;  4HK1 A;  2NTI B; 
#chains in the Genus database with same CATH homology
 3A1J B;  1W60 A;  4L60 A;  3U5Z F;  3P87 A;  3P91 A;  5DA7 A;  2IZO B;  2IO4 A;  3LX2 A;  1U76 A;  3U60 F;  1RXZ A;  2HIK B;  2IX2 C;  3V60 B;  5B7O A;  3F1W A;  3G65 B;  1GE8 A;  4TR6 A;  3LX1 A;  3TBL A;  2OD8 A;  2IJX A;  4ZTD A;  3U61 F;  1PLR A;  3K4X A;  2Z0L A;  1UL1 A;  2ZVL A;  1B77 A;  3HSL X;  2IO4 B;  5E0T A;  3A2F B;  4L6P A;  5JNE D;  1DML A;  3I2M X;  2HII A;  1IZ5 A;  2HII C;  2ZVW A;  2IX2 A;  5CFK A;  1YYP A;  1IZ4 A;  1RXM A;  1CZD A;  5IXA A;  4RJF A;  1PLQ A;  3P83 A;  5DAI A;  5A6D A;  1B8H A;  2ZVV A;  1U7B A;  3V62 B;  3AIX A;  1RWZ A;  3WGW A;  4D2G A;  2HII B;  3GGR A;  3GGR C;  1T6L A;  2IX2 B;  3FDS D;  5H0T A;  2AVT A;  1SXJ F;  3IFV A;  2ZVM A;  5IY4 A;  3AIZ A;  3AIZ C;  4CS5 A;  2NTI A;  2NTI C;  3A1J A;  2AWA A;  3A1J C;  5E0U A;  4YHR A;  3V61 B;  1UD9 A;  5AUJ A;  5E0V A;  3GPM A;  3HI8 A;  1AXC A;  2ZVK A;  2IZO C;  3AIX B;  3GPN A;  1VYM A;  5HAC A;  5IWD A;  1VYJ A;  3GGR B;  2HIK A;  2HIK C;  3VKX A;  3G65 A;  3FDS C;  3G65 C;  1ISQ A;  4HK1 A;  2NTI 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...

5JNED

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations