3CD6 | Genus

Total Genus 11

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	11
sequence length	53
structure length	53
Chain Sequence	RECDYCGTDIEPGTGTMFVHKDGATTHFCSSKCENNADLGREARNLEWTDTAR

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__44815141324551666__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__44815141324551666__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3cd6/U/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__44815141324551666__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"44815141324551666","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3cd6/U/"

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__44815141324551666__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d264199ba4486f6f0553966/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d264199ba4486f6f0553966/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d264199ba4486f6f0553966/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/5d264199ba4486f6f0553966/pdb.gz): 193 ms

reading 53 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

53 atoms created

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

Time for creating model: 14 ms

Adding embedded #jmolscript: select ({0:52});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	Ribosome
publication title	Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. pubmed doi rcsb
molecule keywords	50S ribosomal protein L2P
total genus	11
structure length	53
sequence length	53
ec nomenclature
pdb deposition date	2008-02-26

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
U	PF01246	Ribosomal_L24e	Ribosomal protein L24e

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

cath code	Class	Architecture	Topology	Homology	Domain
2.30.170.20	Mainly Beta	Roll	Ribosomal Protein L24e; Chain: T;	Ribosomal Protein L24e; Chain: T;	3cd6U00

1YJWU 2QA4U 1YJ9U 1K8AV 1W2BT 1VQ7U 3CMEU 1KC8V 1VQKU 1VQ6U 3I55U 1K73V 3OW2T 1Q82V 1M90V 1KQST 3CCSU 3CCLU 3I56U 3CCEU 1S72U 2QEXU 1VQ9U 1YITU 1YJNU 1VQ8U 3CCMU 1QVFT 3G6EU 1QVGT 1Q86V 3CC2U 1JJ2T 1VQLU 3CXCT 1Q7YV 1VQNU 1VQ4U 1YHQU 1N8RV 3CPWT 1K9MV 2OTLU 3CCVU 1Q81V 1M1KV 3CC7U 1NJIV 3CMAU 5AN9G 1VQMU 2OTJU 3CCQU 3G4SU 1VQOU 3CCJU 3CD6U 1YIJU 1KD1V 3G71U 1VQPU 1YI2U 3CC4U 3CCUU 3CCRU 1VQ5U
chains in the Genus database with same CATH superfamily

1YJWU 3CMEU 1VQ6U 1K73V 3OW2T 1QVGT 1Q86V 3CXCT 1Q7YV 1YHQU 1N8RV 3CCVU 1Q81V 1M1KV 5DM6U 2OTJU 1K8AV 3CD6U 1W2BT 1VQ7U 1KC8V 1VQ9U 1QVFT 1VQNU 3CPWT 1K9MV 3ABRA 3CC7U 3CMAU 3CCQU 1VQOU 3CCJU 1JJDA 3G71U 1VQ5U 1YJ9U 3AO0A 1KQST 1M90V 3CCSU 3I56U 3CCEU 4UY8X 3ABOA 1YJNU 1VQ8U 1JJ2T 3ANYA 1NJIV 1VQMU 5H1SY 3J7ZX 3G4SU 1YIJU 1VQPU 1YI2U 3CCRU 2QA4U 3ABQA 1VQKU 2JZ6A 3I55U 1Q82V 2QEZA 3CCLU 1S72U 2QEXU 1YITU 3CCMU 3G6EU 3CC2U 1VQLU 1VQ4U 5MLCY 3ABSA 2OTLU 5AN9G 1KD1V 3CC4U 3CCUU
chains in the Genus database with same CATH topology

1YJWU 2QA4U 1YJ9U 1K8AV 1W2BT 1VQ7U 3CMEU 1KC8V 1VQKU 1VQ6U 3I55U 1K73V 3OW2T 1Q82V 1M90V 1KQST 3CCSU 3CCLU 3I56U 3CCEU 1S72U 2QEXU 1VQ9U 1YITU 1YJNU 1VQ8U 3CCMU 1QVFT 3G6EU 1QVGT 1Q86V 3CC2U 1JJ2T 1VQLU 3CXCT 1Q7YV 1VQNU 1VQ4U 1YHQU 1N8RV 3CPWT 1K9MV 2OTLU 3CCVU 1Q81V 1M1KV 3CC7U 1NJIV 3CMAU 5AN9G 1VQMU 2OTJU 3CCQU 3G4SU 1VQOU 3CCJU 1JJDA 3CD6U 1YIJU 1KD1V 3G71U 1VQPU 1YI2U 3CC4U 3CCUU 3CCRU 1VQ5U
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 1YJW U;  2QA4 U;  1YJ9 U;  1K8A V;  1W2B T;  1VQ7 U;  3CME U;  1KC8 V;  1VQK U;  1VQ6 U;  3I55 U;  1K73 V;  3OW2 T;  1Q82 V;  1M90 V;  1KQS T;  3CCS U;  3CCL U;  3I56 U;  3CCE U;  1S72 U;  2QEX U;  1VQ9 U;  1YIT U;  1YJN U;  1VQ8 U;  3CCM U;  1QVF T;  3G6E U;  1QVG T;  1Q86 V;  3CC2 U;  1JJ2 T;  1VQL U;  3CXC T;  1Q7Y V;  1VQN U;  1VQ4 U;  1YHQ U;  1N8R V;  3CPW T;  1K9M V;  2OTL U;  3CCV U;  1Q81 V;  1M1K V;  3CC7 U;  1NJI V;  3CMA U;  5AN9 G;  1VQM U;  2OTJ U;  3CCQ U;  3G4S U;  1VQO U;  3CCJ U;  3CD6 U;  1YIJ U;  1KD1 V;  3G71 U;  1VQP U;  1YI2 U;  3CC4 U;  3CCU U;  3CCR U;  1VQ5 U; 
#chains in the Genus database with same CATH topology
 1YJW U;  3CME U;  1VQ6 U;  1K73 V;  3OW2 T;  1QVG T;  1Q86 V;  3CXC T;  1Q7Y V;  1YHQ U;  1N8R V;  3CCV U;  1Q81 V;  1M1K V;  5DM6 U;  2OTJ U;  1K8A V;  3CD6 U;  1W2B T;  1VQ7 U;  1KC8 V;  1VQ9 U;  1QVF T;  1VQN U;  3CPW T;  1K9M V;  3ABR A;  3CC7 U;  3CMA U;  3CCQ U;  1VQO U;  3CCJ U;  1JJD A;  3G71 U;  1VQ5 U;  1YJ9 U;  3AO0 A;  1KQS T;  1M90 V;  3CCS U;  3I56 U;  3CCE U;  4UY8 X;  3ABO A;  1YJN U;  1VQ8 U;  1JJ2 T;  3ANY A;  1NJI V;  1VQM U;  5H1S Y;  3J7Z X;  3G4S U;  1YIJ U;  1VQP U;  1YI2 U;  3CCR U;  2QA4 U;  3ABQ A;  1VQK U;  2JZ6 A;  3I55 U;  1Q82 V;  2QEZ A;  3CCL U;  1S72 U;  2QEX U;  1YIT U;  3CCM U;  3G6E U;  3CC2 U;  1VQL U;  1VQ4 U;  5MLC Y;  3ABS A;  2OTL U;  5AN9 G;  1KD1 V;  3CC4 U;  3CCU U; 
#chains in the Genus database with same CATH homology
 1YJW U;  2QA4 U;  1YJ9 U;  1K8A V;  1W2B T;  1VQ7 U;  3CME U;  1KC8 V;  1VQK U;  1VQ6 U;  3I55 U;  1K73 V;  3OW2 T;  1Q82 V;  1M90 V;  1KQS T;  3CCS U;  3CCL U;  3I56 U;  3CCE U;  1S72 U;  2QEX U;  1VQ9 U;  1YIT U;  1YJN U;  1VQ8 U;  3CCM U;  1QVF T;  3G6E U;  1QVG T;  1Q86 V;  3CC2 U;  1JJ2 T;  1VQL U;  3CXC T;  1Q7Y V;  1VQN U;  1VQ4 U;  1YHQ U;  1N8R V;  3CPW T;  1K9M V;  2OTL U;  3CCV U;  1Q81 V;  1M1K V;  3CC7 U;  1NJI V;  3CMA U;  5AN9 G;  1VQM U;  2OTJ U;  3CCQ U;  3G4S U;  1VQO U;  3CCJ U;  1JJD A;  3CD6 U;  1YIJ U;  1KD1 V;  3G71 U;  1VQP U;  1YI2 U;  3CC4 U;  3CCU U;  3CCR U;  1VQ5 U;

...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...

3CD6U

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations