4GR7 | Genus

Total Genus 47

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	47
sequence length	173
structure length	173
Chain Sequence	GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSARVDSGCRMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVIDFS

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__134889450951076__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__134889450951076__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4GR7/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__134889450951076__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"134889450951076","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4GR7/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__134889450951076__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d002ead97ef2b69938628f6/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d002ead97ef2b69938628f6/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d002ead97ef2b69938628f6/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/5d002ead97ef2b69938628f6/pdb.gz): 354 ms

reading 173 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

173 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:172});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	Structural protein
source organism	Homo sapiens
publication title	The human W42R gamma D-crystallin mutant structure provides a link between congenital and age-related cataracts. pubmed doi rcsb
molecule keywords	Gamma-crystallin D
total genus	47
structure length	173
sequence length	173
chains with identical sequence	X
ec nomenclature
pdb deposition date	2012-08-24

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00030	Crystall	Beta/Gamma crystallin

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.20.10	Mainly Beta	Sandwich	Gamma-B Crystallin; domain 1	Crystallins	4gr7A02
2.60.20.10	Mainly Beta	Sandwich	Gamma-B Crystallin; domain 1	Crystallins	4gr7A01

4W9BA 1PRSA 4JGFA 4AKAA 1GCSA 2JDGA 1ZWOA 4W9AA 1AMMA 1M8UA 1YHPA 2BB2A 1E7NA 1DSLA 3ENTA 4IAUA 4PSPA 4EL6A 2BV2A 3IAJA 3SNYA 1H4AX 3HZBA 1HA4A 1ZWMA 2M3TA 4NI3A 1BLBA 2M3UA 4PSRA 5HT8A 1ZIQA 1GAMA 2G98A 2A5MA 1HK0X 2M3CA 3CW3A 3SO1A 3ENUA 1ELPA 5HT9A 4GR7A 1BD7A 1I5IA 3LWKA 1OKIA 1YTQA 1A45A 2K1WA 2KP5A 3I9HA 1AG4A 2B1OA 2DADA 2JDFA 1ZIRA 2KFBA 2V2UA 3SNZA 2NBRA 1ZIEA 2K1XA 1A7HA 1HDFA 1NPSA 3HZ2A 4FD9A 1A5DA 3SO0A 3QK3A 1PRRA 1ZGTA 4GCRA
chains in the Genus database with same CATH superfamily

1GH5A 1AMMA 2BB2A 4IAUA 4PSPA 1G6EA 4PSRA 1ZIQA 2A5MA 1HK0X 4GR7A 1I5IA 1YTQA 1A7HA 1NPSA 2BV2A 4W9BA 1GCSA 2JDGA 1M8UA 1F53A 3IAJA 2M3TA 1BLBA 1GAMA 2M3CA 3CW3A 5HT9A 1ELPA 2KP5A 3I9HA 2V2UA 2DADA 1ZIRA 3SNZA 2K1XA 1A5DA 1ZGTA 4GCRA 4AKAA 1PRSA 1ZWOA 1YHPA 1E7NA 3ENTA 1HA4A 5HT8A 2G98A 1BD7A 1OKIA 1A45A 1WKTA 2K1WA 2NBRA 1ZIEA 3HZ2A 3QK3A 1BHUA 3UJZA 4JGFA 4W9AA 1DSLA 4EL6A 3SNYA 1H4AX 3HZBA 1ZWMA 4NI3A 2M3UA 1C01A 3SO1A 3ENUA 3LWKA 1AG4A 2B1OA 2JDFA 2KFBA 1HDFA 4FD9A 3SO0A 1PRRA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4W9B A;  1PRS A;  4JGF A;  4AKA A;  1GCS A;  2JDG A;  1ZWO A;  4W9A A;  1AMM A;  1M8U A;  1YHP A;  2BB2 A;  1E7N A;  1DSL A;  3ENT A;  4IAU A;  4PSP A;  4EL6 A;  2BV2 A;  3IAJ A;  3SNY A;  1H4A X;  3HZB A;  1HA4 A;  1ZWM A;  2M3T A;  4NI3 A;  1BLB A;  2M3U A;  4PSR A;  5HT8 A;  1ZIQ A;  1GAM A;  2G98 A;  2A5M A;  1HK0 X;  2M3C A;  3CW3 A;  3SO1 A;  3ENU A;  1ELP A;  5HT9 A;  4GR7 A;  1BD7 A;  1I5I A;  3LWK A;  1OKI A;  1YTQ A;  1A45 A;  2K1W A;  2KP5 A;  3I9H A;  1AG4 A;  2B1O A;  2DAD A;  2JDF A;  1ZIR A;  2KFB A;  2V2U A;  3SNZ A;  2NBR A;  1ZIE A;  2K1X A;  1A7H A;  1HDF A;  1NPS A;  3HZ2 A;  4FD9 A;  1A5D A;  3SO0 A;  3QK3 A;  1PRR A;  1ZGT A;  4GCR A; 
#chains in the Genus database with same CATH topology
 1GH5 A;  1AMM A;  2BB2 A;  4IAU A;  4PSP A;  1G6E A;  4PSR A;  1ZIQ A;  2A5M A;  1HK0 X;  4GR7 A;  1I5I A;  1YTQ A;  1A7H A;  1NPS A;  2BV2 A;  4W9B A;  1GCS A;  2JDG A;  1M8U A;  1F53 A;  3IAJ A;  2M3T A;  1BLB A;  1GAM A;  2M3C A;  3CW3 A;  5HT9 A;  1ELP A;  2KP5 A;  3I9H A;  2V2U A;  2DAD A;  1ZIR A;  3SNZ A;  2K1X A;  1A5D A;  1ZGT A;  4GCR A;  4AKA A;  1PRS A;  1ZWO A;  1YHP A;  1E7N A;  3ENT A;  1HA4 A;  5HT8 A;  2G98 A;  1BD7 A;  1OKI A;  1A45 A;  1WKT A;  2K1W A;  2NBR A;  1ZIE A;  3HZ2 A;  3QK3 A;  1BHU A;  3UJZ A;  4JGF A;  4W9A A;  1DSL A;  4EL6 A;  3SNY A;  1H4A X;  3HZB A;  1ZWM A;  4NI3 A;  2M3U A;  1C01 A;  3SO1 A;  3ENU A;  3LWK A;  1AG4 A;  2B1O A;  2JDF A;  2KFB A;  1HDF A;  4FD9 A;  3SO0 A;  1PRR A; 
#chains in the Genus database with same CATH homology
 4W9B A;  1PRS A;  4JGF A;  4AKA A;  1GCS A;  2JDG A;  1ZWO A;  4W9A A;  1AMM A;  1M8U A;  1YHP A;  2BB2 A;  1E7N A;  1DSL A;  3ENT A;  4IAU A;  4PSP A;  4EL6 A;  2BV2 A;  3IAJ A;  3SNY A;  1H4A X;  3HZB A;  1HA4 A;  1ZWM A;  2M3T A;  4NI3 A;  1BLB A;  2M3U A;  4PSR A;  5HT8 A;  1ZIQ A;  1GAM A;  2G98 A;  2A5M A;  1HK0 X;  2M3C A;  3CW3 A;  3SO1 A;  3ENU A;  1ELP A;  5HT9 A;  4GR7 A;  1BD7 A;  1I5I A;  3LWK A;  1OKI A;  1YTQ A;  1A45 A;  2K1W A;  2KP5 A;  3I9H A;  1AG4 A;  2B1O A;  2DAD A;  2JDF A;  1ZIR A;  2KFB A;  2V2U A;  3SNZ A;  2NBR A;  1ZIE A;  2K1X A;  1A7H A;  1HDF A;  1NPS A;  3HZ2 A;  4FD9 A;  1A5D A;  3SO0 A;  3QK3 A;  1PRR A;  1ZGT A;  4GCR 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...

4GR7A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations