3UD1 | Genus

Total Genus 76

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	76
sequence length	322
structure length	320
Chain Sequence	GFLVSFMVDARGGSMRGSRHNGLRVVIPPRTCAAPTRITCRLVKPQKLSTPPPLAEEEGLASRIIALGPTGAQFLSPVIVEIPHFASHGRGDRELVVLRSENGSVWKEHRSRYGESYLDQILNGMDEELGSLEELEKRVCRIITTDFPLYFVIMSRLCQDYDIIGPEGGSLKSKLVPLVQATFPENAVTKRVKLALQAQPVPDELVTKLLGNQATFSPIVTVEPRRRKFHRPIGLRIPLPPSWTDNPRDSGEGDTSLRLLCSVIGGTDQAQWEDITGTTKLVYANECANFTTNVSARFWLSDCPRTAEAVNFATLLYKEL

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__4817244718452005__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__4817244718452005__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3UD1/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__4817244718452005__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"4817244718452005","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3UD1/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__4817244718452005__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d03307ce2ceffa6962ff55b/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d03307ce2ceffa6962ff55b/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d03307ce2ceffa6962ff55b/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/5d03307ce2ceffa6962ff55b/pdb.gz): 1048 ms

reading 320 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

320 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:319});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	Protein binding
source organism	Homo sapiens
publication title	Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin. pubmed doi rcsb
molecule keywords	Ankyrin-1
total genus	76
structure length	320
sequence length	322
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2011-10-27

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00791	ZU5	ZU5 domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.220.30	Mainly Beta	Sandwich	Chondroitinase Ac; Chain A, domain 3	Chondroitinase Ac; Chain A, domain 3	3ud1A01
2.60.220.30	Mainly Beta	Sandwich	Chondroitinase Ac; Chain A, domain 3	Chondroitinase Ac; Chain A, domain 3	3ud1A02

2KXSA 3UD2A 3KBTC 3F59A 3UD1A 3KBUC 2KXRA 4D8OA
chains in the Genus database with same CATH superfamily

1LXMA 2KXSA 4DLOA 4D6FA 2E24A 1CB8A 1LXKA 1N7QA 1I8QA 1RWHA 1J0NA 2WMIB 3F59A 3KBTC 2E22A 3PQIA 1RWCA 3KBUC 2WMIA 1HN0A 2BRWA 2WMKA 2WDAA 3UD2A 4DLQA 1F1SA 1X1HA 4D6GA 1J0MA 4D6HA 4D1JA 1OJOA 1OJNA 1N7NA 2X03A 1N7PA 4D8OA 2BRVX 4D6EA 4D71A 1X1IA 2WCOA 1N7OA 1RW9A 4D6CA 4D6JA 3UD1A 1OJPA 3QR8A 1RWFA 4D6DA 2BRPA 2KXRA 2WMHA 1OJMA 2WMJA 2WMFA 4D1IA 1RWAA 1W3YA 1HMWA 4D72A 1C82A 1HMUA 1F9GA 2Q1FA 1HM2A 1N7RA 1RWGA 3U7VA 1HM3A 4D6IA 2WMGA 1X1JA 1EGUA 1LOHA
chains in the Genus database with same CATH topology

2KXSA 3UD2A 4DLOA 4DLQA 3KBTC 3F59A 3QR8A 3UD1A 3PQIA 3KBUC 2KXRA 4D8OA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2KXS A;  3UD2 A;  3KBT C;  3F59 A;  3UD1 A;  3KBU C;  2KXR A;  4D8O A; 
#chains in the Genus database with same CATH topology
 1LXM A;  2KXS A;  4DLO A;  4D6F A;  2E24 A;  1CB8 A;  1LXK A;  1N7Q A;  1I8Q A;  1RWH A;  1J0N A;  2WMI B;  3F59 A;  3KBT C;  2E22 A;  3PQI A;  1RWC A;  3KBU C;  2WMI A;  1HN0 A;  2BRW A;  2WMK A;  2WDA A;  3UD2 A;  4DLQ A;  1F1S A;  1X1H A;  4D6G A;  1J0M A;  4D6H A;  4D1J A;  1OJO A;  1OJN A;  1N7N A;  2X03 A;  1N7P A;  4D8O A;  2BRV X;  4D6E A;  4D71 A;  1X1I A;  2WCO A;  1N7O A;  1RW9 A;  4D6C A;  4D6J A;  3UD1 A;  1OJP A;  3QR8 A;  1RWF A;  4D6D A;  2BRP A;  2KXR A;  2WMH A;  1OJM A;  2WMJ A;  2WMF A;  4D1I A;  1RWA A;  1W3Y A;  1HMW A;  4D72 A;  1C82 A;  1HMU A;  1F9G A;  2Q1F A;  1HM2 A;  1N7R A;  1RWG A;  3U7V A;  1HM3 A;  4D6I A;  2WMG A;  1X1J A;  1EGU A;  1LOH A; 
#chains in the Genus database with same CATH homology
 2KXS A;  3UD2 A;  4DLO A;  4DLQ A;  3KBT C;  3F59 A;  3QR8 A;  3UD1 A;  3PQI A;  3KBU C;  2KXR A;  4D8O 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...

3UD1A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations