3FDS | Genus

Total Genus 65

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	65
sequence length	249
structure length	249
Chain Sequence	MVKIVYPNAKDFFSFINSITNVTDSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVKKILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVGEEMRISTEEDKIKIEAGEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL

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__7017461447004933__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__7017461447004933__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3FDS/C/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__7017461447004933__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"7017461447004933","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3FDS/C/"

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__7017461447004933__ 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	Transferase
source organism	Sulfolobus solfataricus
publication title	Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA pubmed doi rcsb
molecule keywords	DNA polymerase IV
total genus	65
structure length	249
sequence length	249
ec nomenclature
pdb deposition date	2008-11-26

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
C	PF00705	PCNA_N	Proliferating cell nuclear antigen, N-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	3fdsC01

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

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

3FDSC

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations