4AQY | Genus

Total Genus 52

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	52
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__3812394756850725__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__3812394756850725__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4AQY/D/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__3812394756850725__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3812394756850725","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4AQY/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__3812394756850725__ 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	Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin. pubmed doi rcsb
molecule keywords	16S RIBOSOMAL RNA
total genus	52
structure length	208
sequence length	208
ec nomenclature
pdb deposition date	2012-04-20

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	4aqyD01
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	4aqyD02

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

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

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

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

4AQYD

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations