4G0A | Genus

Total Genus 101

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	101
sequence length	312
structure length	312
Chain Sequence	AELACFCYPHLENDSYKFIPFNNLAIKAMLTAKVDKKDMDKFYDSIIYGIAPPPQFKKRYNTNDNSRGMNFETIMFTKVAMLICEALNSLKVTQANVSNVLSRVVSIRHLENLVIRKENPQDILFHSKDLLLKSTLIAIGQSKEIETTITAEGGEIVFQNAAFTMWKLTYLEHQLMPILDQNFIEYKVTLNEDKPISDVHVKELVAELRWQYNKFAVITHGKGHYRIVKYSSVANHADRVYATFKSNVKTGVNNDFNLLDQRIIWQNWYAFTSSMKQGNTLDVCKRLLFQKMKPEKNPFKGLSTDRKMDEVS

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__7540049888937386__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__7540049888937386__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4G0A/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__7540049888937386__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"7540049888937386","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4G0A/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__7540049888937386__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d26690bfbd60e6f14eb9b8c/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d26690bfbd60e6f14eb9b8c/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d26690bfbd60e6f14eb9b8c/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/5d26690bfbd60e6f14eb9b8c/pdb.gz): 666 ms

reading 312 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

312 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:311});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	Hydrolase/rna
source organism	Simian 11 rotavirus
publication title	Crystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals Specific Recognition of 5' GG Sequence for RTPase Activity. pubmed doi rcsb
molecule keywords	Non-structural protein 2
total genus	101
structure length	312
sequence length	312
chains with identical sequence	B, C, D
ec nomenclature	ec 3.6.4.-:
pdb deposition date	2012-07-09

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02509	Rota_NS35	Rotavirus non-structural protein 35

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.428.20	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	Rotavirus NSP2 fragment, C-terminal domain	4g0aA02
3.90.1400.10	Alpha Beta	Alpha-Beta Complex	Rotavirus NSP2 fragment, N-terminal domain	Rotavirus NSP2 fragment, N-terminal domain	4g0aA01

2R7JA 2R7CA 4G0AA 2R7PA 4G0JA 1L9VA 2GU0A 2R8FA
chains in the Genus database with same CATH superfamily

6RHNA 1KPCA 1Z84A 4NJYA 3O1XA 4G0JA 1RZYA 5IPBA 2H39A 4I5WA 4RHNA 3IMIA 3OHEA 1KPBA 1L9VA 4EQGA 3O1ZA 5IN3A 4NJXA 4NDGA 2R7CA 2FHIA 2R7PA 3RHNA 1KPEA 3OXKA 1AV5A 3OJ7A 5CS2A 3WO5A 4NK0A 2GU0A 1XMMA 1ST0A 5EMTA 1ST4A 4EQEA 2R8FA 1ZWJA 5IPCA 4NDFA 4XBAA 1FHIA 4QDVA 2Q4HA 3R6FA 6FITA 4I5VA 2EO4A 4QEBA 3O1CA 1HXQA 1GUQA 4ZKLA 3ANOA 1Y23A 1XMLA 3FITA 4QDEA 3I4SA 3N1TA 5IPEA 1EMSA 3L7XA 4NJZA 3NRDA 3P0TA 4INCA 4INIA 3I24A 1HXPA 4ZKVA 1KPAA 1GUPA 3SP4A 3BL9A 4I5TA 5I2EA 4NDIA 3SZQA 3O0MA 1VLRA 4ZGLA 5ED3A 3QGZA 5FITA 5RHNA 5IPDA 2LJWA 3LB5A 5BV3A 2POFA 3OMFA 3KSVA 3N1SA 5I2FA 5ED6A 4EQHA 3BL7A 2OIKA 1FITA 4YKLB 2R7JA 4G0AA 2Q4LA 4NDHA 4FITA 4EGUA 3SPLA 3SPDA 3TW2A 2FITA 1KPFA 3BLAA
chains in the Genus database with same CATH topology

2R7JA 2R7CA 4G0AA 2R7PA 4G0JA 1L9VA 2GU0A 2R8FA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2R7J A;  2R7C A;  4G0A A;  2R7P A;  4G0J A;  1L9V A;  2GU0 A;  2R8F A; 
#chains in the Genus database with same CATH topology
 6RHN A;  1KPC A;  1Z84 A;  4NJY A;  3O1X A;  4G0J A;  1RZY A;  5IPB A;  2H39 A;  4I5W A;  4RHN A;  3IMI A;  3OHE A;  1KPB A;  1L9V A;  4EQG A;  3O1Z A;  5IN3 A;  4NJX A;  4NDG A;  2R7C A;  2FHI A;  2R7P A;  3RHN A;  1KPE A;  3OXK A;  1AV5 A;  3OJ7 A;  5CS2 A;  3WO5 A;  4NK0 A;  2GU0 A;  1XMM A;  1ST0 A;  5EMT A;  1ST4 A;  4EQE A;  2R8F A;  1ZWJ A;  5IPC A;  4NDF A;  4XBA A;  1FHI A;  4QDV A;  2Q4H A;  3R6F A;  6FIT A;  4I5V A;  2EO4 A;  4QEB A;  3O1C A;  1HXQ A;  1GUQ A;  4ZKL A;  3ANO A;  1Y23 A;  1XML A;  3FIT A;  4QDE A;  3I4S A;  3N1T A;  5IPE A;  1EMS A;  3L7X A;  4NJZ A;  3NRD A;  3P0T A;  4INC A;  4INI A;  3I24 A;  1HXP A;  4ZKV A;  1KPA A;  1GUP A;  3SP4 A;  3BL9 A;  4I5T A;  5I2E A;  4NDI A;  3SZQ A;  3O0M A;  1VLR A;  4ZGL A;  5ED3 A;  3QGZ A;  5FIT A;  5RHN A;  5IPD A;  2LJW A;  3LB5 A;  5BV3 A;  2POF A;  3OMF A;  3KSV A;  3N1S A;  5I2F A;  5ED6 A;  4EQH A;  3BL7 A;  2OIK A;  1FIT A;  4YKL B;  2R7J A;  4G0A A;  2Q4L A;  4NDH A;  4FIT A;  4EGU A;  3SPL A;  3SPD A;  3TW2 A;  2FIT A;  1KPF A;  3BLA A; 
#chains in the Genus database with same CATH homology
 2R7J A;  2R7C A;  4G0A A;  2R7P A;  4G0J A;  1L9V A;  2GU0 A;  2R8F 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...

4G0AA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations