1I8C | Genus

Total Genus 9

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	9
sequence length	94
structure length	94
Chain Sequence	DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFEDVGHSTDARELSKTYIIGELHPDDRSKIAKPSETL

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__053229824075243__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__053229824075243__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1I8C/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__053229824075243__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"053229824075243","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1I8C/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__053229824075243__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfb53b401f6a4b23ac96715/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfb53b401f6a4b23ac96715/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfb53b401f6a4b23ac96715/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/5cfb53b401f6a4b23ac96715/pdb.gz): 557 ms

reading 94 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

94 atoms created

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

Time for creating model: 17 ms

Adding embedded #jmolscript: select ({0:93});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	Structural and dynamic perturbations induced by heme binding in cytochrome b5. pubmed doi rcsb
molecule keywords	CYTOCHROME B5
molecule tags	Electron transport
source organism	Rattus norvegicus
total genus	9
structure length	94
sequence length	94
ec nomenclature
pdb deposition date	2001-03-13

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00173	Cyt-b5	Cytochrome b5-like Heme/Steroid binding domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.10.120.10	Alpha Beta	Roll	Flavocytochrome B2; Chain A, domain 1	Cytochrome b5-like heme/steroid binding domain	1i8cA00

1NX7A 2KEOA 1IETA 1SOXA 3KS0A 1CXYA 1ICCA 1AW3A 1AWPA 1M2MA 3NERA 3X35A 2M33A 1LCOA 1B5AA 3X32A 2I96A 1EHBA 1HKOA 1B5MA 4B8NA 1I8CA 1IB7A 2AXXA 4X8YA 4HILA 1SH4A 1M20A 1I5UA 1LR6A 1BFXA 1LJ0A 3OZZB 1M59A 1LQXA 1BLVA 1B5BA 1LTDA 1T0GA 1X3XA 2OZ0A 3LF5A 1FCBA 1MJ4A 3MUSA 1U9MA 1DO9A 1KBIA 1AQAA 1LDCA 1MNYA 1I87A 2I89A 2IBJA 1EUEA 1U9UA 1IEUA 1J0QA 1CYOA 4HINA 3X33A 3X34A 1M2IA 1AXXA 1ES1A 1F03A 1J03A 1F04A 1JEXA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1NX7 A;  2KEO A;  1IET A;  1SOX A;  3KS0 A;  1CXY A;  1ICC A;  1AW3 A;  1AWP A;  1M2M A;  3NER A;  3X35 A;  2M33 A;  1LCO A;  1B5A A;  3X32 A;  2I96 A;  1EHB A;  1HKO A;  1B5M A;  4B8N A;  1I8C A;  1IB7 A;  2AXX A;  4X8Y A;  4HIL A;  1SH4 A;  1M20 A;  1I5U A;  1LR6 A;  1BFX A;  1LJ0 A;  3OZZ B;  1M59 A;  1LQX A;  1BLV A;  1B5B A;  1LTD A;  1T0G A;  1X3X A;  2OZ0 A;  3LF5 A;  1FCB A;  1MJ4 A;  3MUS A;  1U9M A;  1DO9 A;  1KBI A;  1AQA A;  1LDC A;  1MNY A;  1I87 A;  2I89 A;  2IBJ A;  1EUE A;  1U9U A;  1IEU A;  1J0Q A;  1CYO A;  4HIN A;  3X33 A;  3X34 A;  1M2I A;  1AXX A;  1ES1 A;  1F03 A;  1J03 A;  1F04 A;  1JEX A; 
#chains in the Genus database with same CATH topology
 1NX7 A;  2KEO A;  1IET A;  1SOX A;  3KS0 A;  1CXY A;  1ICC A;  1AW3 A;  1AWP A;  1M2M A;  3NER A;  3X35 A;  2M33 A;  1LCO A;  1B5A A;  3X32 A;  2I96 A;  1EHB A;  1HKO A;  1B5M A;  4B8N A;  1I8C A;  1IB7 A;  2AXX A;  4X8Y A;  4HIL A;  1SH4 A;  1M20 A;  1I5U A;  1LR6 A;  1BFX A;  1LJ0 A;  3OZZ B;  1M59 A;  1LQX A;  1BLV A;  1B5B A;  1LTD A;  1T0G A;  1X3X A;  2OZ0 A;  3LF5 A;  1FCB A;  1MJ4 A;  3MUS A;  1U9M A;  1DO9 A;  1KBI A;  1AQA A;  1LDC A;  1MNY A;  1I87 A;  2I89 A;  2IBJ A;  1EUE A;  1U9U A;  1IEU A;  1J0Q A;  1CYO A;  4HIN A;  3X33 A;  3X34 A;  1M2I A;  1AXX A;  1ES1 A;  1F03 A;  1J03 A;  1F04 A;  1JEX A; 
#chains in the Genus database with same CATH homology
 1NX7 A;  2KEO A;  1IET A;  1SOX A;  3KS0 A;  1CXY A;  1ICC A;  1AW3 A;  1AWP A;  1M2M A;  3NER A;  3X35 A;  2M33 A;  1LCO A;  1B5A A;  3X32 A;  2I96 A;  1EHB A;  1HKO A;  1B5M A;  4B8N A;  1I8C A;  1IB7 A;  2AXX A;  4X8Y A;  4HIL A;  1SH4 A;  1M20 A;  1I5U A;  1LR6 A;  1BFX A;  1LJ0 A;  3OZZ B;  1M59 A;  1LQX A;  1BLV A;  1B5B A;  1LTD A;  1T0G A;  1X3X A;  2OZ0 A;  3LF5 A;  1FCB A;  1MJ4 A;  3MUS A;  1U9M A;  1DO9 A;  1KBI A;  1AQA A;  1LDC A;  1MNY A;  1I87 A;  2I89 A;  2IBJ A;  1EUE A;  1U9U A;  1IEU A;  1J0Q A;  1CYO A;  4HIN A;  3X33 A;  3X34 A;  1M2I A;  1AXX A;  1ES1 A;  1F03 A;  1J03 A;  1F04 A;  1JEX 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...

1I8CA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations