2K3Q | Genus

Total Genus 34

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	34
sequence length	118
structure length	118
Chain Sequence	GSEQQDLDDLAQVILSAVTSNTDTSKSARAQALSTALASSLADLLISESSGSSYQTQISALTNILSDCFVTTTGSNNPAFVSRVQTLIAVLSQSSSNAISGATGGSAFAQSQAFQQSA

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__956564180020025__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__956564180020025__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2K3Q/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__956564180020025__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"956564180020025","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2K3Q/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__956564180020025__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd4adb81a2fe2a04b23ddb/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd4adb81a2fe2a04b23ddb/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd4adb81a2fe2a04b23ddb/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/5cfd4adb81a2fe2a04b23ddb/pdb.gz): 525 ms

reading 118 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

118 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:117});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	Nephila antipodiana
publication title	Solution structure of eggcase silk protein and its implications for silk fiber formation pubmed doi rcsb
molecule keywords	TuSp1
total genus	34
structure length	118
sequence length	118
ec nomenclature
pdb deposition date	2008-05-15

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF16763	Spidroin_N	Major ampullate spidroin 1, spider silk protein 1, N-term

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.274.70	Mainly Alpha	Orthogonal Bundle	Enzyme I; Chain A, domain 2	Enzyme I; Chain A, domain 2	2k3qA00

2LPIA 3LRDA 2LTHA 2MX8A 2MX9A 3LR2A 3LR8A 5IZ2A 4FBSA 3LR6A 2LPJA 2K3QA 2N3EA
chains in the Genus database with same CATH superfamily

4C5SA 3GTGA 1Y1WA 2EZCA 2K3QA 4C5UA 2HWGA 1IW7D 3FKIA 1EZAA 2N1DB 2E2HA 4CEJA 3GTLA 1I3QA 4CQ5A 3U4QA 4C2MA 2A6ED 2NVYA 2MQAA 1WCMA 2E2IA 3GTOA 2R92A 4BAAA 3U44A 2R7ZA 4C5RA 1TWAA 2VK9A 2Y0NA 2R93A 2B63A 4V2QA 2X0OA 2MP0A 1TWHA 3GTJA 2JA6A 1TWCA 2LPJA 2LPIA 2X0QA 1TWGA 1Y1VA 2NVXA 1Y2MA 4C6GA 1K83A 2A6HD 4CEIA 1ZYMA 1I6VD 3EZEA 1HQMD 2X0PA 1SFOA 2MX8A 1I50A 3EZAA 3CQZA 3GTQA 3GTKA 1T6JA 2A68D 2O5JD 2MX9A 3H0GA 2FIPA 2HROA 2LYIA 3GTMA 2N3EA 2AQLA 2K3OA 3LR8A 2VUMA 2JA5A 4BABA 2F5JA 3LRDA 2YIIA 2YU9A 3GTPA 3EZBA 1R9TA 1EZBA 2A69D 2CW0D 1TWFA 1ZYRD 1T6PA 4V2RA 1W27A 5IZ2A 3LR6A 1YNJD 2LTHA 2FIOA 2BE5D 2JA7A 1SMYD 4FBSA 3NZ4A 2K3NA 4CEHA 4QIWA 2LKMB 2EZBA 3LR2A 2EZAA 1YNND
chains in the Genus database with same CATH topology

3GTGA 1Y1WA 2K3QA 1IW7D 3FKIA 2N1DB 2E2HA 4CEJA 3GTLA 1I3QA 3U4QA 4C2MA 2A6ED 2NVYA 2MQAA 1WCMA 2E2IA 3GTOA 2R92A 3U44A 2R7ZA 1TWAA 2VK9A 2Y0NA 2R93A 2B63A 2X0OA 1TWHA 3GTJA 2JA6A 1TWCA 2LPJA 2LPIA 2X0QA 1TWGA 1Y1VA 2NVXA 1K83A 2A6HD 4CEIA 1I6VD 1HQMD 2X0PA 1SFOA 2MX8A 1I50A 3CQZA 3GTQA 3GTKA 2A68D 2O5JD 2MX9A 3H0GA 2FIPA 2LYIA 3GTMA 2N3EA 2AQLA 2K3OA 3LR8A 2VUMA 2JA5A 2F5JA 3LRDA 2YU9A 3GTPA 1R9TA 2A69D 2CW0D 1TWFA 1ZYRD 5IZ2A 3LR6A 1YNJD 2LTHA 2FIOA 2BE5D 2JA7A 1SMYD 4FBSA 2K3NA 4CEHA 4QIWA 2LKMB 3LR2A 1YNND
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2LPI A;  3LRD A;  2LTH A;  2MX8 A;  2MX9 A;  3LR2 A;  3LR8 A;  5IZ2 A;  4FBS A;  3LR6 A;  2LPJ A;  2K3Q A;  2N3E A; 
#chains in the Genus database with same CATH topology
 4C5S A;  3GTG A;  1Y1W A;  2EZC A;  2K3Q A;  4C5U A;  2HWG A;  1IW7 D;  3FKI A;  1EZA A;  2N1D B;  2E2H A;  4CEJ A;  3GTL A;  1I3Q A;  4CQ5 A;  3U4Q A;  4C2M A;  2A6E D;  2NVY A;  2MQA A;  1WCM A;  2E2I A;  3GTO A;  2R92 A;  4BAA A;  3U44 A;  2R7Z A;  4C5R A;  1TWA A;  2VK9 A;  2Y0N A;  2R93 A;  2B63 A;  4V2Q A;  2X0O A;  2MP0 A;  1TWH A;  3GTJ A;  2JA6 A;  1TWC A;  2LPJ A;  2LPI A;  2X0Q A;  1TWG A;  1Y1V A;  2NVX A;  1Y2M A;  4C6G A;  1K83 A;  2A6H D;  4CEI A;  1ZYM A;  1I6V D;  3EZE A;  1HQM D;  2X0P A;  1SFO A;  2MX8 A;  1I50 A;  3EZA A;  3CQZ A;  3GTQ A;  3GTK A;  1T6J A;  2A68 D;  2O5J D;  2MX9 A;  3H0G A;  2FIP A;  2HRO A;  2LYI A;  3GTM A;  2N3E A;  2AQL A;  2K3O A;  3LR8 A;  2VUM A;  2JA5 A;  4BAB A;  2F5J A;  3LRD A;  2YII A;  2YU9 A;  3GTP A;  3EZB A;  1R9T A;  1EZB A;  2A69 D;  2CW0 D;  1TWF A;  1ZYR D;  1T6P A;  4V2R A;  1W27 A;  5IZ2 A;  3LR6 A;  1YNJ D;  2LTH A;  2FIO A;  2BE5 D;  2JA7 A;  1SMY D;  4FBS A;  3NZ4 A;  2K3N A;  4CEH A;  4QIW A;  2LKM B;  2EZB A;  3LR2 A;  2EZA A;  1YNN D; 
#chains in the Genus database with same CATH homology
 3GTG A;  1Y1W A;  2K3Q A;  1IW7 D;  3FKI A;  2N1D B;  2E2H A;  4CEJ A;  3GTL A;  1I3Q A;  3U4Q A;  4C2M A;  2A6E D;  2NVY A;  2MQA A;  1WCM A;  2E2I A;  3GTO A;  2R92 A;  3U44 A;  2R7Z A;  1TWA A;  2VK9 A;  2Y0N A;  2R93 A;  2B63 A;  2X0O A;  1TWH A;  3GTJ A;  2JA6 A;  1TWC A;  2LPJ A;  2LPI A;  2X0Q A;  1TWG A;  1Y1V A;  2NVX A;  1K83 A;  2A6H D;  4CEI A;  1I6V D;  1HQM D;  2X0P A;  1SFO A;  2MX8 A;  1I50 A;  3CQZ A;  3GTQ A;  3GTK A;  2A68 D;  2O5J D;  2MX9 A;  3H0G A;  2FIP A;  2LYI A;  3GTM A;  2N3E A;  2AQL A;  2K3O A;  3LR8 A;  2VUM A;  2JA5 A;  2F5J A;  3LRD A;  2YU9 A;  3GTP A;  1R9T A;  2A69 D;  2CW0 D;  1TWF A;  1ZYR D;  5IZ2 A;  3LR6 A;  1YNJ D;  2LTH A;  2FIO A;  2BE5 D;  2JA7 A;  1SMY D;  4FBS A;  2K3N A;  4CEH A;  4QIW A;  2LKM B;  3LR2 A;  1YNN D;

...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...

2K3QA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations