3L0X | Genus

Total Genus 28

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	28
sequence length	163
structure length	163
Chain Sequence	MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMIT

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__517274030526835__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__517274030526835__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3L0X/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__517274030526835__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"517274030526835","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3L0X/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__517274030526835__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cff691055a2e70cf143d622/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cff691055a2e70cf143d622/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cff691055a2e70cf143d622/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/5cff691055a2e70cf143d622/pdb.gz): 143 ms

reading 163 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

163 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:162});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	Replication
source organism	Saccharomyces cerevisiae
publication title	Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange. pubmed doi rcsb
molecule keywords	Proliferating cell nuclear antigen
total genus	28
structure length	163
sequence length	163
ec nomenclature
pdb deposition date	2009-12-10

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	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
3.10.150.10	Alpha Beta	Roll	DNA Polymerase III; Chain A, domain 2	DNA Polymerase III, subunit A, domain 2	3l0xA00

4K3QA 4N94A 3L0XA 3PGEB 4N96A 4PNVA 4N97A 3P16A 4TR6A 3D1FA 5FRQA 2XURA 3T0PA 3Q4KA 4K3KA 4K3MA 4MJRA 4OVGA 1JQJA 4N99A 4OVHA 4K3LA 5FVEA 1JQLA 3D1EA 4TR8A 5AGVA 3BEPA 4RKIA 4N98A 4PNWA 4TSZA 3QSBB 1UNNA 4K3RA 3QSBA 3Q4JA 4N95A 3PWEA 4K74A 4TR7A 4MJQA 3L10A 3RB9A 3L0WA 4S3IA 3F1VA 5AH4A 4N9AA 4PNUA 5AGUA 4K3PA 1VPKA 2AVTA 3D1GA 4K3SA 4TRTA 1MMIA 2AWAA 4OVFA 1OK7A 2POLA 4K3OA 4MJPA 3Q4LA 5AH2A
chains in the Genus database with same CATH superfamily

4K3QA 4N94A 3L0XA 3PGEB 4N96A 4PNVA 3PGEA 4N97A 3P16A 4TR6A 3D1FA 5FRQA 2XURA 3T0PA 3Q4KA 4K3KA 4K3MA 4MJRA 4OVGA 1JQJA 4N99A 4OVHA 4K3LA 5FVEA 1JQLA 3D1EA 4TR8A 5AGVA 5AH2A 3BEPA 4RKIA 4N98A 4PNWA 4TSZA 3QSBB 1UNNA 4K3RA 3QSBA 3Q4JA 4N95A 3PWEA 3L10B 4K74A 4TR7A 4MJQA 3L10A 3L0WB 3RB9A 3L0WA 4S3IA 3F1VA 5AH4A 4N9AA 4PNUA 5AGUA 4K3PA 1VPKA 2AVTA 3D1GA 4K3SA 4TRTA 1MMIA 2AWAA 4OVFA 1OK7A 2POLA 4K3OA 4MJPA 3Q4LA 3L0XB
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4K3Q A;  4N94 A;  3L0X A;  3PGE B;  4N96 A;  4PNV A;  4N97 A;  3P16 A;  4TR6 A;  3D1F A;  5FRQ A;  2XUR A;  3T0P A;  3Q4K A;  4K3K A;  4K3M A;  4MJR A;  4OVG A;  1JQJ A;  4N99 A;  4OVH A;  4K3L A;  5FVE A;  1JQL A;  3D1E A;  4TR8 A;  5AGV A;  3BEP A;  4RKI A;  4N98 A;  4PNW A;  4TSZ A;  3QSB B;  1UNN A;  4K3R A;  3QSB A;  3Q4J A;  4N95 A;  3PWE A;  4K74 A;  4TR7 A;  4MJQ A;  3L10 A;  3RB9 A;  3L0W A;  4S3I A;  3F1V A;  5AH4 A;  4N9A A;  4PNU A;  5AGU A;  4K3P A;  1VPK A;  2AVT A;  3D1G A;  4K3S A;  4TRT A;  1MMI A;  2AWA A;  4OVF A;  1OK7 A;  2POL A;  4K3O A;  4MJP A;  3Q4L A;  5AH2 A; 
#chains in the Genus database with same CATH topology
 4K3Q A;  4N94 A;  3L0X A;  3PGE B;  4N96 A;  4PNV A;  3PGE A;  4N97 A;  3P16 A;  4TR6 A;  3D1F A;  5FRQ A;  2XUR A;  3T0P A;  3Q4K A;  4K3K A;  4K3M A;  4MJR A;  4OVG A;  1JQJ A;  4N99 A;  4OVH A;  4K3L A;  5FVE A;  1JQL A;  3D1E A;  4TR8 A;  5AGV A;  5AH2 A;  3BEP A;  4RKI A;  4N98 A;  4PNW A;  4TSZ A;  3QSB B;  1UNN A;  4K3R A;  3QSB A;  3Q4J A;  4N95 A;  3PWE A;  3L10 B;  4K74 A;  4TR7 A;  4MJQ A;  3L10 A;  3L0W B;  3RB9 A;  3L0W A;  4S3I A;  3F1V A;  5AH4 A;  4N9A A;  4PNU A;  5AGU A;  4K3P A;  1VPK A;  2AVT A;  3D1G A;  4K3S A;  4TRT A;  1MMI A;  2AWA A;  4OVF A;  1OK7 A;  2POL A;  4K3O A;  4MJP A;  3Q4L A;  3L0X B; 
#chains in the Genus database with same CATH homology
 4K3Q A;  4N94 A;  3L0X A;  3PGE B;  4N96 A;  4PNV A;  4N97 A;  3P16 A;  4TR6 A;  3D1F A;  5FRQ A;  2XUR A;  3T0P A;  3Q4K A;  4K3K A;  4K3M A;  4MJR A;  4OVG A;  1JQJ A;  4N99 A;  4OVH A;  4K3L A;  5FVE A;  1JQL A;  3D1E A;  4TR8 A;  5AGV A;  3BEP A;  4RKI A;  4N98 A;  4PNW A;  4TSZ A;  3QSB B;  1UNN A;  4K3R A;  3QSB A;  3Q4J A;  4N95 A;  3PWE A;  4K74 A;  4TR7 A;  4MJQ A;  3L10 A;  3RB9 A;  3L0W A;  4S3I A;  3F1V A;  5AH4 A;  4N9A A;  4PNU A;  5AGU A;  4K3P A;  1VPK A;  2AVT A;  3D1G A;  4K3S A;  4TRT A;  1MMI A;  2AWA A;  4OVF A;  1OK7 A;  2POL A;  4K3O A;  4MJP A;  3Q4L A;  5AH2 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...

3L0XA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations