4NYI | Genus

Total Genus 176

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	176
sequence length	481
structure length	472
Chain Sequence	QMRLPSADVYRFAEPDSEENIIFEENMAGIPIIKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIAHNITFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNPR

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__1164171415313535__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__1164171415313535__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4NYI/S/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__1164171415313535__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"1164171415313535","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4NYI/S/"

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__1164171415313535__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0086fd6775487c7fa26052/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0086fd6775487c7fa26052/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0086fd6775487c7fa26052/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/5d0086fd6775487c7fa26052/pdb.gz): 1136 ms

reading 472 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

472 atoms created

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

Time for creating model: 52 ms

Adding embedded #jmolscript: select ({0:471});backbone only;select *;

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

molecule tags	Signaling protein
source organism	Homo sapiens
publication title	Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange. pubmed doi rcsb
molecule keywords	GTPase HRas
total genus	176
structure length	472
sequence length	481
ec nomenclature
pdb deposition date	2013-12-10

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
S	PF00617	RasGEF	RasGEF domain
S	PF00618	RasGEF_N	RasGEF N-terminal motif

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein; Chain S, domain 2	Ras guanine-nucleotide exchange factors catalytic domain	4nyiS02
1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein; Chain S, domain 1	Son of sevenless (SoS) protein Chain: S domain 1	4nyiS01

3CF6E 4US2S 5CM9A 4F7ZA 4JGWA 4URZS 4URYS 4URUS 4MH0E 1NVVS 1NVXS 1NVWS 2BYVE 3T6AA 4MGYE 4MGIE 4URWS 4NYIS 1XD2C 4NYJS 3T6GA 4US0S 1BKDS 3KSYA 3QXLA 4URXS 2IJES 4NYMS 4MGZE 4US1S 1NVUS 1XD4A 2II0A 4MGKE 5CM8A 4L9MA 4URVS
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 3CF6 E;  4US2 S;  5CM9 A;  4F7Z A;  4JGW A;  4URZ S;  4URY S;  4URU S;  4MH0 E;  1NVV S;  1NVX S;  1NVW S;  2BYV E;  3T6A A;  4MGY E;  4MGI E;  4URW S;  4NYI S;  1XD2 C;  4NYJ S;  3T6G A;  4US0 S;  1BKD S;  3KSY A;  3QXL A;  4URX S;  2IJE S;  4NYM S;  4MGZ E;  4US1 S;  1NVU S;  1XD4 A;  2II0 A;  4MGK E;  5CM8 A;  4L9M A;  4URV S; 
#chains in the Genus database with same CATH topology
 3CF6 E;  4US2 S;  5CM9 A;  4F7Z A;  4JGW A;  4URZ S;  4URY S;  4URU S;  4MH0 E;  1NVV S;  1NVX S;  1NVW S;  2BYV E;  3T6A A;  4MGY E;  4MGI E;  4URW S;  4NYI S;  1XD2 C;  4NYJ S;  3T6G A;  4US0 S;  1BKD S;  3KSY A;  3QXL A;  4URX S;  2IJE S;  4NYM S;  4MGZ E;  4US1 S;  1NVU S;  1XD4 A;  2II0 A;  4MGK E;  5CM8 A;  4L9M A;  4URV S; 
#chains in the Genus database with same CATH homology
 3CF6 E;  4US2 S;  5CM9 A;  4F7Z A;  4JGW A;  4URZ S;  4URY S;  4URU S;  4MH0 E;  1NVV S;  1NVX S;  1NVW S;  2BYV E;  3T6A A;  4MGY E;  4MGI E;  4URW S;  4NYI S;  1XD2 C;  4NYJ S;  3T6G A;  4US0 S;  1BKD S;  3KSY A;  3QXL A;  4URX S;  2IJE S;  4NYM S;  4MGZ E;  4US1 S;  1NVU S;  1XD4 A;  2II0 A;  4MGK E;  5CM8 A;  4L9M A;  4URV S;

...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...

4NYIS

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations