1J5E | Genus

Total Genus 59

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	59
sequence length	208
structure length	208
Chain Sequence	GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR

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__067978371954934__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__067978371954934__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1J5E/D/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__067978371954934__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"067978371954934","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1J5E/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__067978371954934__ 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	Ribosome
publication title	Structure of the 30S ribosomal subunit. pubmed doi rcsb
molecule keywords	16S ribosomal RNA
total genus	59
structure length	208
sequence length	208
ec nomenclature
pdb deposition date	2002-04-08

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
D	PF00163	Ribosomal_S4	Ribosomal protein S4/S9 N-terminal domain
D	PF01479	S4	S4 domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.1050.10	Mainly Alpha	Orthogonal Bundle	Ribosomal Protein S4 Delta 41; Chain A, domain 1	Ribosomal Protein S4 Delta 41; Chain A, domain 1	1j5eD01
3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A	RNA-binding S4 domain	1j5eD02

4LF9D 1IBMD 4DR3D 4DR4D 4DV1D 4JYAD 4LF6D 2UUCD 2KTLA 5LMND 1N32D 1XNRD 5LMUD 1C06A 1H3FA 4LGTA 2UXBD 4NXMD 2VQFD 4LF4D 4DV5D 4DR7D 4JI3D 1J5ED 4DUZD 4JV5D 1IBKD 1HNXD 4YHHD 5BR8D 1KSLA 2E5LD 4DV2D 1HNZD 2UUAD 2UUBD 2ZM6D 4LFAD 4JI1D 4X64D 4LF5D 4JI7D 2UXDD 4JI2D 4X62D 2ISTA 4LFBD 4JI4D 1KSVA 4DV4D 4K0KD 4B3TD 4YY3D 1JH3A 4DR1D 3OTOD 4B3SD 4KHPD 4X66D 4DV3D 4JI6D 4B3RD 1XMOD 1C05A 3T1HD 4DV7D 4OX9D 4LF7D 3KBGA 4DR6D 4DUYD 2UU9D 1IBLD 1KSKA 1P9KA 4GKJD 4DV6D 3T1YD 4JI5D 4NXND 2K6PA 4OUDA 2JANA 1FJGD 1H3EA 2HHHD 3DH3A 2F4VD 4GKKD 2VQED 4AQYD 1N36D 4DR5D 1FKAD 1HR0D 5IWAD 3HP7A 1N34D 1HNWD 4LFCD 4B3MD 1XNQD 1VIOA 4X65D 1I94D 2UXCD 4JI8D 1DM9A 4JI0D 1XMQD 4LF8D 4DR2D 4DV0D 1N33D
chains in the Genus database with same CATH superfamily

4LF9D 1IBMD 3ONHA 4DR3D 4DR4D 3J80E 4DV1D 3ONGA 4JYAD 4LF6D 2UUCD 1Y8XB 2KTLA 4II3A 5LMND 1N32D 1XNRD 5LMUD 3JAME 1C06A 1H3FA 4LGTA 4NNJA 5A2QE 2UXBD 4NXMD 2VQFD 4LF4D 5FQ2B 4DV5D 3J81E 2NVUB 4DR7D 4JI3D 3KYCB 1J5ED 4DUZD 4JV5D 1IBKD 1HNXD 4YHHD 5BR8D 1KSLA 2E5LD 4DV2D 1HNZD 4II2A 2UUAD 2UUBD 2ZM6D 4LFAD 4JI1D 4X64D 4LF5D 4JI7D 2UXDD 3CMMA 4JI2D 4X62D 2ZTBA 2ISTA 4LFBD 4JI4D 4W5VB 1KSVA 4DV4D 4K0KD 4B3TD 5KNLA 4YY3D 2I1SA 1JH3A 4DR1D 3OTOD 5IT9E 1Y8QB 3J7AF 4B3SD 4KHPD 4X66D 4DV3D 4JI6D 4B3RD 1XMOD 1C05A 3T1HD 4DV7D 4OX9D 3FN1A 4LF7D 3KBGA 4DR6D 4DUYD 2UU9D 1IBLD 1KSKA 1P9KA 4GKJD 4DV6D 3T1YD 4JI5D 2LQ7A 4NXND 2K6PA 4OUDA 2JANA 3KYDB 1FJGD 1H3EA 2HHHD 3DH3A 2F4VD 4GKKD 5FLXE 2VQED 4AQYD 1N36D 4DR5D 1FKAD 1HR0D 5IWAD 3HP7A 1N34D 1HNWD 4LFCD 2L3NA 4B3MD 1XNQD 1VIOA 4X65D 1I94D 2UXCD 4JI8D 1DM9A 5LL6S 4JI0D 1Y8RB 1XMQD 4LF8D 4DR2D 4DV0D 1N33D
chains in the Genus database with same CATH topology

4LF9D 1IBMD 4DR3D 4DR4D 4DV1D 4JYAD 4LF6D 2UUCD 2KTLA 5LMND 1N32D 1XNRD 5LMUD 1C06A 1H3FA 4LGTA 2UXBD 4NXMD 2VQFD 4LF4D 4DV5D 4DR7D 4JI3D 1J5ED 4DUZD 4JV5D 1IBKD 1HNXD 4YHHD 5BR8D 1KSLA 2E5LD 4DV2D 1HNZD 2UUAD 2UUBD 2ZM6D 4LFAD 4JI1D 4X64D 4LF5D 4JI7D 2UXDD 4JI2D 4X62D 2ISTA 4LFBD 4JI4D 1KSVA 4DV4D 4K0KD 4B3TD 4YY3D 1JH3A 4DR1D 3OTOD 4B3SD 4KHPD 4X66D 4DV3D 4JI6D 4B3RD 1XMOD 1C05A 3T1HD 4DV7D 4OX9D 4LF7D 3KBGA 4DR6D 4DUYD 2UU9D 1IBLD 1KSKA 1P9KA 4GKJD 4DV6D 3T1YD 4JI5D 4NXND 2K6PA 4OUDA 2JANA 1FJGD 1H3EA 2HHHD 3DH3A 2F4VD 4GKKD 2VQED 4AQYD 1N36D 4DR5D 1FKAD 1HR0D 5IWAD 3HP7A 1N34D 1HNWD 4LFCD 2L3NA 4B3MD 1XNQD 1VIOA 4X65D 1I94D 2UXCD 4JI8D 1DM9A 4JI0D 1XMQD 4LF8D 4DR2D 4DV0D 1N33D
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 4LF9 D;  1IBM D;  4DR3 D;  4DR4 D;  4DV1 D;  4JYA D;  4LF6 D;  2UUC D;  2KTL A;  5LMN D;  1N32 D;  1XNR D;  5LMU D;  1C06 A;  1H3F A;  4LGT A;  2UXB D;  4NXM D;  2VQF D;  4LF4 D;  4DV5 D;  4DR7 D;  4JI3 D;  1J5E D;  4DUZ D;  4JV5 D;  1IBK D;  1HNX D;  4YHH D;  5BR8 D;  1KSL A;  2E5L D;  4DV2 D;  1HNZ D;  2UUA D;  2UUB D;  2ZM6 D;  4LFA D;  4JI1 D;  4X64 D;  4LF5 D;  4JI7 D;  2UXD D;  4JI2 D;  4X62 D;  2IST A;  4LFB D;  4JI4 D;  1KSV A;  4DV4 D;  4K0K D;  4B3T D;  4YY3 D;  1JH3 A;  4DR1 D;  3OTO D;  4B3S D;  4KHP D;  4X66 D;  4DV3 D;  4JI6 D;  4B3R D;  1XMO D;  1C05 A;  3T1H D;  4DV7 D;  4OX9 D;  4LF7 D;  3KBG A;  4DR6 D;  4DUY D;  2UU9 D;  1IBL D;  1KSK A;  1P9K A;  4GKJ D;  4DV6 D;  3T1Y D;  4JI5 D;  4NXN D;  2K6P A;  4OUD A;  2JAN A;  1FJG D;  1H3E A;  2HHH D;  3DH3 A;  2F4V D;  4GKK D;  2VQE D;  4AQY D;  1N36 D;  4DR5 D;  1FKA D;  1HR0 D;  5IWA D;  3HP7 A;  1N34 D;  1HNW D;  4LFC D;  4B3M D;  1XNQ D;  1VIO A;  4X65 D;  1I94 D;  2UXC D;  4JI8 D;  1DM9 A;  4JI0 D;  1XMQ D;  4LF8 D;  4DR2 D;  4DV0 D;  1N33 D; 
#chains in the Genus database with same CATH topology
 4LF9 D;  1IBM D;  3ONH A;  4DR3 D;  4DR4 D;  3J80 E;  4DV1 D;  3ONG A;  4JYA D;  4LF6 D;  2UUC D;  1Y8X B;  2KTL A;  4II3 A;  5LMN D;  1N32 D;  1XNR D;  5LMU D;  3JAM E;  1C06 A;  1H3F A;  4LGT A;  4NNJ A;  5A2Q E;  2UXB D;  4NXM D;  2VQF D;  4LF4 D;  5FQ2 B;  4DV5 D;  3J81 E;  2NVU B;  4DR7 D;  4JI3 D;  3KYC B;  1J5E D;  4DUZ D;  4JV5 D;  1IBK D;  1HNX D;  4YHH D;  5BR8 D;  1KSL A;  2E5L D;  4DV2 D;  1HNZ D;  4II2 A;  2UUA D;  2UUB D;  2ZM6 D;  4LFA D;  4JI1 D;  4X64 D;  4LF5 D;  4JI7 D;  2UXD D;  3CMM A;  4JI2 D;  4X62 D;  2ZTB A;  2IST A;  4LFB D;  4JI4 D;  4W5V B;  1KSV A;  4DV4 D;  4K0K D;  4B3T D;  5KNL A;  4YY3 D;  2I1S A;  1JH3 A;  4DR1 D;  3OTO D;  5IT9 E;  1Y8Q B;  3J7A F;  4B3S D;  4KHP D;  4X66 D;  4DV3 D;  4JI6 D;  4B3R D;  1XMO D;  1C05 A;  3T1H D;  4DV7 D;  4OX9 D;  3FN1 A;  4LF7 D;  3KBG A;  4DR6 D;  4DUY D;  2UU9 D;  1IBL D;  1KSK A;  1P9K A;  4GKJ D;  4DV6 D;  3T1Y D;  4JI5 D;  2LQ7 A;  4NXN D;  2K6P A;  4OUD A;  2JAN A;  3KYD B;  1FJG D;  1H3E A;  2HHH D;  3DH3 A;  2F4V D;  4GKK D;  5FLX E;  2VQE D;  4AQY D;  1N36 D;  4DR5 D;  1FKA D;  1HR0 D;  5IWA D;  3HP7 A;  1N34 D;  1HNW D;  4LFC D;  2L3N A;  4B3M D;  1XNQ D;  1VIO A;  4X65 D;  1I94 D;  2UXC D;  4JI8 D;  1DM9 A;  5LL6 S;  4JI0 D;  1Y8R B;  1XMQ D;  4LF8 D;  4DR2 D;  4DV0 D;  1N33 D; 
#chains in the Genus database with same CATH homology
 4LF9 D;  1IBM D;  4DR3 D;  4DR4 D;  4DV1 D;  4JYA D;  4LF6 D;  2UUC D;  2KTL A;  5LMN D;  1N32 D;  1XNR D;  5LMU D;  1C06 A;  1H3F A;  4LGT A;  2UXB D;  4NXM D;  2VQF D;  4LF4 D;  4DV5 D;  4DR7 D;  4JI3 D;  1J5E D;  4DUZ D;  4JV5 D;  1IBK D;  1HNX D;  4YHH D;  5BR8 D;  1KSL A;  2E5L D;  4DV2 D;  1HNZ D;  2UUA D;  2UUB D;  2ZM6 D;  4LFA D;  4JI1 D;  4X64 D;  4LF5 D;  4JI7 D;  2UXD D;  4JI2 D;  4X62 D;  2IST A;  4LFB D;  4JI4 D;  1KSV A;  4DV4 D;  4K0K D;  4B3T D;  4YY3 D;  1JH3 A;  4DR1 D;  3OTO D;  4B3S D;  4KHP D;  4X66 D;  4DV3 D;  4JI6 D;  4B3R D;  1XMO D;  1C05 A;  3T1H D;  4DV7 D;  4OX9 D;  4LF7 D;  3KBG A;  4DR6 D;  4DUY D;  2UU9 D;  1IBL D;  1KSK A;  1P9K A;  4GKJ D;  4DV6 D;  3T1Y D;  4JI5 D;  4NXN D;  2K6P A;  4OUD A;  2JAN A;  1FJG D;  1H3E A;  2HHH D;  3DH3 A;  2F4V D;  4GKK D;  2VQE D;  4AQY D;  1N36 D;  4DR5 D;  1FKA D;  1HR0 D;  5IWA D;  3HP7 A;  1N34 D;  1HNW D;  4LFC D;  2L3N A;  4B3M D;  1XNQ D;  1VIO A;  4X65 D;  1I94 D;  2UXC D;  4JI8 D;  1DM9 A;  4JI0 D;  1XMQ D;  4LF8 D;  4DR2 D;  4DV0 D;  1N33 D;

...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...

1J5ED

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations