1BXN | Genus

Total Genus 23

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	23
sequence length	129
structure length	129
Chain Sequence	MRITQGTFSFLPELTDEQITKQLEYCLNQGWAVGLEYTDDPHPRNTYWEMFGLPMFDLRDAAGILMEINNARNTFPNHYIRVTAFDSTHTVESVVMSFIVNRPADEPGFRLVRQEEPGRTLRYSIESYA

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__863922352944758__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__863922352944758__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1BXN/I/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__863922352944758__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"863922352944758","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1BXN/I/"

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__863922352944758__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfad174e346b1957a0b60a2/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfad174e346b1957a0b60a2/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfad174e346b1957a0b60a2/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/5cfad174e346b1957a0b60a2/pdb.gz): 279 ms

reading 129 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

129 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:128});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

publication title	The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded beta-barrel formed by beta-strands from four subunits. pubmed doi rcsb
molecule keywords	PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
molecule tags	Lyase
source organism	Cupriavidus necator
total genus	23
structure length	129
sequence length	129
chains with identical sequence	J, K, L
ec nomenclature	ec 4.1.1.39: Ribulose-bisphosphate carboxylase.
pdb deposition date	1998-10-06

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
I	PF00101	RuBisCO_small	Ribulose bisphosphate carboxylase, small chain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	1bxnI00

1RCXC 1UPPI 1UW9C 1RBLI 1IR1S 4RUBS 8RUCI 2V63I 1RLDS 1BWVS 1GK8I 1UZDC 3AXMS 3AXKS 4HHHS 1SVDM 1RSCI 1RBOC 1UZHC 1AA1C 1EJ7S 1BXNI 1WDDS 2VDII 4F0MB 4F0HB 1IR21 2V69I 2V68I 2YBVB 3ZXWB 3RUBS 2V6AI 4F0KB 2V67I 1RLCS 1UPMC 1RXOC 4MKVS 1IWAB 2VDHI 1AUSS 1RCOC 1UWAC
chains in the Genus database with same CATH superfamily

1RCXC 2HW8A 1UPPI 2FHZA 1UW9C 1RBLI 1IR1S 4QGBA 4RUBS 8RUCI 1AD2A 2V63I 5DM60 1RLDS 4QVIA 1BWVS 4QG3A 1GK8I 1UZDC 3U4MA 1ZHOA 5DM70 3FPNA 3AXMS 3AXKS 4HHHS 4F9TA 4REOA 1SVDM 1RSCI 1RBOC 1UZHC 1AA1C 1EJ7S 1BXNI 1WDDS 2VDII 3ZQJA 4F0MB 1IR21 2V69I 4F0HB 2V68I 2YBVB 4DFCB 3U56A 1U63A 3ZXWB 2DFXI 1DWUA 3RUBS 3UMYA 1I2AA 2V6AI 1CJSA 3TG8A 4F0KB 2V67I 1RLCS 1UPMC 1RXOC 4MKVS 1IWAB 2VDHI 3QOYA 4LQ4A 1AUSS 1RCOC 1UWAC 1MZPA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1RCX C;  1UPP I;  1UW9 C;  1RBL I;  1IR1 S;  4RUB S;  8RUC I;  2V63 I;  1RLD S;  1BWV S;  1GK8 I;  1UZD C;  3AXM S;  3AXK S;  4HHH S;  1SVD M;  1RSC I;  1RBO C;  1UZH C;  1AA1 C;  1EJ7 S;  1BXN I;  1WDD S;  2VDI I;  4F0M B;  4F0H B;  1IR2 1;  2V69 I;  2V68 I;  2YBV B;  3ZXW B;  3RUB S;  2V6A I;  4F0K B;  2V67 I;  1RLC S;  1UPM C;  1RXO C;  4MKV S;  1IWA B;  2VDH I;  1AUS S;  1RCO C;  1UWA C; 
#chains in the Genus database with same CATH topology
 1RCX C;  2HW8 A;  1UPP I;  2FHZ A;  1UW9 C;  1RBL I;  1IR1 S;  4QGB A;  4RUB S;  8RUC I;  1AD2 A;  2V63 I;  5DM6 0;  1RLD S;  4QVI A;  1BWV S;  4QG3 A;  1GK8 I;  1UZD C;  3U4M A;  1ZHO A;  5DM7 0;  3FPN A;  3AXM S;  3AXK S;  4HHH S;  4F9T A;  4REO A;  1SVD M;  1RSC I;  1RBO C;  1UZH C;  1AA1 C;  1EJ7 S;  1BXN I;  1WDD S;  2VDI I;  3ZQJ A;  4F0M B;  1IR2 1;  2V69 I;  4F0H B;  2V68 I;  2YBV B;  4DFC B;  3U56 A;  1U63 A;  3ZXW B;  2DFX I;  1DWU A;  3RUB S;  3UMY A;  1I2A A;  2V6A I;  1CJS A;  3TG8 A;  4F0K B;  2V67 I;  1RLC S;  1UPM C;  1RXO C;  4MKV S;  1IWA B;  2VDH I;  3QOY A;  4LQ4 A;  1AUS S;  1RCO C;  1UWA C;  1MZP A; 
#chains in the Genus database with same CATH homology
 1RCX C;  1UPP I;  1UW9 C;  1RBL I;  1IR1 S;  4RUB S;  8RUC I;  2V63 I;  1RLD S;  1BWV S;  1GK8 I;  1UZD C;  3AXM S;  3AXK S;  4HHH S;  1SVD M;  1RSC I;  1RBO C;  1UZH C;  1AA1 C;  1EJ7 S;  1BXN I;  1WDD S;  2VDI I;  4F0M B;  4F0H B;  1IR2 1;  2V69 I;  2V68 I;  2YBV B;  3ZXW B;  3RUB S;  2V6A I;  4F0K B;  2V67 I;  1RLC S;  1UPM C;  1RXO C;  4MKV S;  1IWA B;  2VDH I;  1AUS S;  1RCO C;  1UWA C;

...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...

1BXNI

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations