1HDF | Genus

Total Genus 26

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	26
sequence length	100
structure length	100
Chain Sequence	SVCKGVSGNPAKGEVFLYKHVNFQGDSWKVTGNVYDFRSVSGLNDVVSSVKVGPNTKAFIFKDDRFNGNFIRLEESSQVTDLTTRNLNDAISSMIVATFE

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__978706568819115__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__978706568819115__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1HDF/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__978706568819115__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"978706568819115","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1HDF/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__978706568819115__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfb509a269bfcb988c9144e/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfb509a269bfcb988c9144e/pdb.gz

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	Physarum polycephalum
publication title	Crystal Structure of the Calcium-Loaded Spherulin 3A Dimer Sheds Light on the Evolution of the Eye Lens Betagamma-Crystallin Domain Fold pubmed doi rcsb
molecule keywords	SPHERULIN 3A
total genus	26
structure length	100
sequence length	100
chains with identical sequence	B
ec nomenclature
pdb deposition date	2000-11-13

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF08964	Crystall_3	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	1hdfA00

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

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

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

1HDFA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations