6AME | Genus

Total Genus 14

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	14
sequence length	66
structure length	66
Chain Sequence	ANQASVVANQLIPINTALTLVAMRSEVVTPVGIPAEDIPRLVSMQVNRAVPLGTTLMPDMVKGYAA

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__984870554289117__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__984870554289117__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/6AME/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__984870554289117__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"984870554289117","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/6AME/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__984870554289117__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d071aaa49ee378865bfb6cc/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d071aaa49ee378865bfb6cc/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d071aaa49ee378865bfb6cc/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/5d071aaa49ee378865bfb6cc/pdb.gz): 2752 ms

reading 66 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

66 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:65});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	Antifreeze protein
source organism	Macrozoarces americanus
publication title	Quantitative and qualitative analysis of type III antifreeze protein structure and function. pubmed doi rcsb
molecule keywords	PROTEIN (ANTIFREEZE PROTEIN TYPE III)
total genus	14
structure length	66
sequence length	66
ec nomenclature
pdb deposition date	1999-01-24

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

cath code	Class	Architecture	Topology	Homology	Domain
3.90.1210.10	Alpha Beta	Alpha-Beta Complex	Type Iii Antifreeze Protein Isoform Hplc 12	Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain	6ameA00

1EKLA 3G8RA 6MSIA 1B7JA 1AMEA 3QF6A 1XUUA 1UCSA 1MSIA 1JABA 3RDNA 3AMEA 3MSIA 5MSIA 1KDEA 3CM4A 1C89A 1WVOA 1B7IA 8AMEA 4IPIA 9AMEA 2JIAA 6AMEA 2LX2A 1KDFA 3FRNA 4IPJA 1XUZA 2LX3A 1VLIA 2ZDRA 1MSJA 7MSIA 7AMEA 1HG7A 9MSIA 4UR4A 1B7KA 2MSIA 1OPSA 4AMEA 2SPGA 3NLAA 2WQPA 4NY6A 2MSJA 1C8AA 2AMEA 1GZIA 8MSIA 4UR6A 4MSIA
chains in the Genus database with same CATH superfamily

1EKLA 3G8RA 6MSIA 1B7JA 1AMEA 3QF6A 1XUUA 1UCSA 1MSIA 1JABA 3LAZA 3AMEA 3MSIA 3RDNA 5MSIA 1KDEA 3CM4A 1C89A 1WVOA 1B7IA 8AMEA 4IPIA 9AMEA 2JIAA 6AMEA 2LX2A 1KDFA 3FRNA 4IPJA 1XUZA 2LX3A 1VLIA 2ZDRA 1MSJA 7MSIA 7AMEA 1HG7A 9MSIA 4UR4A 1B7KA 2MSIA 3K3SA 1OPSA 4AMEA 2SPGA 3NLAA 2WQPA 4NY6A 2MSJA 1C8AA 2AMEA 1GZIA 8MSIA 4UR6A 4MSIA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1EKL A;  3G8R A;  6MSI A;  1B7J A;  1AME A;  3QF6 A;  1XUU A;  1UCS A;  1MSI A;  1JAB A;  3RDN A;  3AME A;  3MSI A;  5MSI A;  1KDE A;  3CM4 A;  1C89 A;  1WVO A;  1B7I A;  8AME A;  4IPI A;  9AME A;  2JIA A;  6AME A;  2LX2 A;  1KDF A;  3FRN A;  4IPJ A;  1XUZ A;  2LX3 A;  1VLI A;  2ZDR A;  1MSJ A;  7MSI A;  7AME A;  1HG7 A;  9MSI A;  4UR4 A;  1B7K A;  2MSI A;  1OPS A;  4AME A;  2SPG A;  3NLA A;  2WQP A;  4NY6 A;  2MSJ A;  1C8A A;  2AME A;  1GZI A;  8MSI A;  4UR6 A;  4MSI A; 
#chains in the Genus database with same CATH topology
 1EKL A;  3G8R A;  6MSI A;  1B7J A;  1AME A;  3QF6 A;  1XUU A;  1UCS A;  1MSI A;  1JAB A;  3LAZ A;  3AME A;  3MSI A;  3RDN A;  5MSI A;  1KDE A;  3CM4 A;  1C89 A;  1WVO A;  1B7I A;  8AME A;  4IPI A;  9AME A;  2JIA A;  6AME A;  2LX2 A;  1KDF A;  3FRN A;  4IPJ A;  1XUZ A;  2LX3 A;  1VLI A;  2ZDR A;  1MSJ A;  7MSI A;  7AME A;  1HG7 A;  9MSI A;  4UR4 A;  1B7K A;  2MSI A;  3K3S A;  1OPS A;  4AME A;  2SPG A;  3NLA A;  2WQP A;  4NY6 A;  2MSJ A;  1C8A A;  2AME A;  1GZI A;  8MSI A;  4UR6 A;  4MSI A; 
#chains in the Genus database with same CATH homology
 1EKL A;  3G8R A;  6MSI A;  1B7J A;  1AME A;  3QF6 A;  1XUU A;  1UCS A;  1MSI A;  1JAB A;  3RDN A;  3AME A;  3MSI A;  5MSI A;  1KDE A;  3CM4 A;  1C89 A;  1WVO A;  1B7I A;  8AME A;  4IPI A;  9AME A;  2JIA A;  6AME A;  2LX2 A;  1KDF A;  3FRN A;  4IPJ A;  1XUZ A;  2LX3 A;  1VLI A;  2ZDR A;  1MSJ A;  7MSI A;  7AME A;  1HG7 A;  9MSI A;  4UR4 A;  1B7K A;  2MSI A;  1OPS A;  4AME A;  2SPG A;  3NLA A;  2WQP A;  4NY6 A;  2MSJ A;  1C8A A;  2AME A;  1GZI A;  8MSI A;  4UR6 A;  4MSI 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...

6AMEA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN