3OQO | Genus

Total Genus 22

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	22
sequence length	87
structure length	86
Chain Sequence	AQKTFKVTADSGIHARPATVLVQTASKYDADVNLEYNGKTVNLKIMGVMSLGIAKGAEITISASGADENDALNALEETMKSEGLGE

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__687260359550694__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__687260359550694__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3OQO/D/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__687260359550694__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"687260359550694","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3OQO/D/"

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__687260359550694__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d20086a2eae9d7cbb9e284f/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d20086a2eae9d7cbb9e284f/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d20086a2eae9d7cbb9e284f/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/5d20086a2eae9d7cbb9e284f/pdb.gz): 463 ms

reading 86 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

86 atoms created

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

Time for creating model: 16 ms

Adding embedded #jmolscript: select ({0:85});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	Transcription/transferase/dna
source organism	Bacillus subtilis
publication title	Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators. pubmed doi rcsb
molecule keywords	Catabolite control protein A
total genus	22
structure length	86
sequence length	87
chains with identical sequence	S
ec nomenclature	ec 2.7.11.-:
pdb deposition date	2010-09-03

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
D	PF00381	PTS-HPr	PTS HPr component phosphorylation site

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1340.10	Alpha Beta	2-Layer Sandwich	Histidine-containing Protein; Chain: A;	HPr-like	3oqoD00

1FU0A 3OQMD 1VRCC 1TXEA 2NZVL 1K1CA 1CM2A 1MO1A 1PCHA 1RZRL 2HIDA 2NZUL 2RLZA 1QR5A 1KKMH 1PTFA 1MU4A 1OPDA 1QFRA 1KA5A 2AK7A 1POHA 3OQND 1JEMA 1GGRB 3EZEB 3IHSA 2OENL 3LE3A 1J6TB 1CM3A 1MO1B 2JELP 1Y4YA 3LFGA 3LE1A 1SPHA 3LE5A 3LNWA 5T17A 1KKLH 2HPRA 3CCDA 1ZVVJ 1HDNA 2XDFC 3OQOD 3EZAB 4XWJB 1PFHA 5T1OA 1Y51A 2LRLD 1Y50A 5T1NA 2FEPS 3EZBB 2LRKD
chains in the Genus database with same CATH superfamily

1FU0A 3OQMD 1VRCC 1TXEA 2NZVL 1K1CA 1CM2A 1MO1A 1PCHA 1RZRL 1J5YA 2HIDA 2NZUL 2RLZA 1QR5A 1KKMH 1PTFA 1MU4A 1OPDA 1QFRA 1KA5A 2AK7A 1POHA 3OQND 1JEMA 1GGRB 3EZEB 3IHSA 2OENL 3LE3A 1J6TB 1CM3A 1MO1B 2JELP 1Y4YA 3LFGA 3LE1A 1SPHA 3LE5A 3LNWA 5T17A 1KKLH 2HPRA 3CCDA 1ZVVJ 1HDNA 2XDFC 3OQOD 3EZAB 4XWJB 1PFHA 5T1OA 1Y51A 2LRLD 1Y50A 5T1NA 2FEPS 3EZBB 2LRKD
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1FU0 A;  3OQM D;  1VRC C;  1TXE A;  2NZV L;  1K1C A;  1CM2 A;  1MO1 A;  1PCH A;  1RZR L;  2HID A;  2NZU L;  2RLZ A;  1QR5 A;  1KKM H;  1PTF A;  1MU4 A;  1OPD A;  1QFR A;  1KA5 A;  2AK7 A;  1POH A;  3OQN D;  1JEM A;  1GGR B;  3EZE B;  3IHS A;  2OEN L;  3LE3 A;  1J6T B;  1CM3 A;  1MO1 B;  2JEL P;  1Y4Y A;  3LFG A;  3LE1 A;  1SPH A;  3LE5 A;  3LNW A;  5T17 A;  1KKL H;  2HPR A;  3CCD A;  1ZVV J;  1HDN A;  2XDF C;  3OQO D;  3EZA B;  4XWJ B;  1PFH A;  5T1O A;  1Y51 A;  2LRL D;  1Y50 A;  5T1N A;  2FEP S;  3EZB B;  2LRK D; 
#chains in the Genus database with same CATH topology
 1FU0 A;  3OQM D;  1VRC C;  1TXE A;  2NZV L;  1K1C A;  1CM2 A;  1MO1 A;  1PCH A;  1RZR L;  1J5Y A;  2HID A;  2NZU L;  2RLZ A;  1QR5 A;  1KKM H;  1PTF A;  1MU4 A;  1OPD A;  1QFR A;  1KA5 A;  2AK7 A;  1POH A;  3OQN D;  1JEM A;  1GGR B;  3EZE B;  3IHS A;  2OEN L;  3LE3 A;  1J6T B;  1CM3 A;  1MO1 B;  2JEL P;  1Y4Y A;  3LFG A;  3LE1 A;  1SPH A;  3LE5 A;  3LNW A;  5T17 A;  1KKL H;  2HPR A;  3CCD A;  1ZVV J;  1HDN A;  2XDF C;  3OQO D;  3EZA B;  4XWJ B;  1PFH A;  5T1O A;  1Y51 A;  2LRL D;  1Y50 A;  5T1N A;  2FEP S;  3EZB B;  2LRK D; 
#chains in the Genus database with same CATH homology
 1FU0 A;  3OQM D;  1VRC C;  1TXE A;  2NZV L;  1K1C A;  1CM2 A;  1MO1 A;  1PCH A;  1RZR L;  2HID A;  2NZU L;  2RLZ A;  1QR5 A;  1KKM H;  1PTF A;  1MU4 A;  1OPD A;  1QFR A;  1KA5 A;  2AK7 A;  1POH A;  3OQN D;  1JEM A;  1GGR B;  3EZE B;  3IHS A;  2OEN L;  3LE3 A;  1J6T B;  1CM3 A;  1MO1 B;  2JEL P;  1Y4Y A;  3LFG A;  3LE1 A;  1SPH A;  3LE5 A;  3LNW A;  5T17 A;  1KKL H;  2HPR A;  3CCD A;  1ZVV J;  1HDN A;  2XDF C;  3OQO D;  3EZA B;  4XWJ B;  1PFH A;  5T1O A;  1Y51 A;  2LRL D;  1Y50 A;  5T1N A;  2FEP S;  3EZB B;  2LRK 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...

3OQOD

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations