3P83 | Genus

Total Genus 63

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	63
sequence length	244
structure length	244
Chain Sequence	MIDVIMTGELLKTVTRAIVALVSEARIHFLEKGLHSRAVDPANVAMVIVDIPKDSFEVYNIDEEKTIGVDMDRIFDISKSISTKDLVELIVEDESTLKVKFGSVEYKVALIDPSAIRKEPRIPELELPAKIVMDAGEFKKAIAAADKISDQVIFRSDKEGFRIEAKGDVDSIVFHMTETELIEFNGGEARSMFSVDYLKEFCKVAGSGDLLTIHLGTNYPVRLVFELVGGRAKVEYILAPRIES

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__267055888246921__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__267055888246921__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3P83/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__267055888246921__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"267055888246921","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3P83/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__267055888246921__ 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	Hydrolase/dna binding protein
source organism	Archaeoglobus fulgidus
publication title	PCNA directs type 2 RNase H activity on DNA replication and repair substrates. pubmed doi rcsb
molecule keywords	DNA polymerase sliding clamp
total genus	63
structure length	244
sequence length	244
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2010-10-13

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00705	PCNA_N	Proliferating cell nuclear antigen, N-terminal domain
A	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	3p83A00

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

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

3P83A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations