5EXR | Genus

Total Genus 98

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	98
sequence length	412
structure length	389
Chain Sequence	METFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAIRTRDYKKTSLAPYVKVFEHFLENLDKSRKGELLK

Loading diagram...

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__5448693158877456__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__5448693158877456__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/5EXR/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__5448693158877456__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"5448693158877456","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/5EXR/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__5448693158877456__ 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

publication title	Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome. pubmed doi rcsb
molecule keywords	DNA primase small subunit
molecule tags	Replication
source organism	Homo sapiens
total genus	98
structure length	389
sequence length	412
chains with identical sequence	E
ec nomenclature
pdb deposition date	2015-11-24

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01896	DNA_primase_S	DNA primase small subunit

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

cath code	Class	Architecture	Topology	Homology	Domain
3.90.920.30	Alpha Beta	Alpha-Beta Complex	DNA primase, PRIM domain	DNA primase, PRIM domain	5exrA00

4MHQA 4LILA 4LIKA 2FARA 4BPXA 4RR2A 4BPWA 4MM2A 5EXRA 4LIMA 2FAOA 1ZT2A 2FAQA 4BPUA
chains in the Genus database with same CATH superfamily

1G71A 4MHQA 1V34A 4LILA 4LIKA 1V33A 2FARA 4BPXA 4RR2A 2ATZA 4MM2A 5EXRA 4LIMA 4BPWA 2FAOA 1ZT2A 2FAQA 4BPUA
chains in the Genus database with same CATH topology

1G71A 4MHQA 1V34A 4LILA 4LIKA 1V33A 2FARA 4BPXA 4RR2A 4BPWA 4MM2A 5EXRA 4LIMA 2FAOA 1ZT2A 2FAQA 4BPUA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 4MHQ A;  4LIL A;  4LIK A;  2FAR A;  4BPX A;  4RR2 A;  4BPW A;  4MM2 A;  5EXR A;  4LIM A;  2FAO A;  1ZT2 A;  2FAQ A;  4BPU A; 
#chains in the Genus database with same CATH topology
 1G71 A;  4MHQ A;  1V34 A;  4LIL A;  4LIK A;  1V33 A;  2FAR A;  4BPX A;  4RR2 A;  2ATZ A;  4MM2 A;  5EXR A;  4LIM A;  4BPW A;  2FAO A;  1ZT2 A;  2FAQ A;  4BPU A; 
#chains in the Genus database with same CATH homology
 1G71 A;  4MHQ A;  1V34 A;  4LIL A;  4LIK A;  1V33 A;  2FAR A;  4BPX A;  4RR2 A;  4BPW A;  4MM2 A;  5EXR A;  4LIM A;  2FAO A;  1ZT2 A;  2FAQ A;  4BPU 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...

5EXRA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations