2D32 | Genus

Total Genus 188

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	188
sequence length	518
structure length	510
Chain Sequence	MIPDVSQALAWLEKHPQALKGIQRGLERETLRVNADGTLATTGHPEALGSALTHKWITTDFAEALLEFITPVDGDIEHMLTFMRDLHRYTARNMGDERMWPLSMPSYIAEGQDIELAQYGTSNTGRFKTLYREGLKNRYGALMQTISGVHYNFSLPMAFWQAKSGADAKEKISAGYFRVIRNYYRFGWVIPYLFGASPAISSSFLTSLPFEKTESGMYYLPYATSLRLSDLGYTNKSQSNLGITFNDLYEYVAGLKQAIKTPSEEYAKIGIEKDGKRLQINSNVLQIENELYAPIRPKRVTRSGESPSDALLRGGIEYIEVRSLDINPFSPIGVDEQQVRFLDLFMVWCALADAPEMSSSELACTRVNWNRVILEGRKPGLTLGIGCETAQFPLPQVGKDLFRDLKRVAQTLDSINGGEAYQKVCDELVACFDNPDLTFSARILRSMIDTGIGGTGKAFAEAYRNLLREEPLEILREEDFVAEREASERRQQEMEAADTEPFAVWLEKHA

Loading diagram...

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__432305956169845__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__432305956169845__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2D32/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__432305956169845__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"432305956169845","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2D32/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__432305956169845__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfcd4437b1f6152d2f022bd/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfcd4437b1f6152d2f022bd/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfcd4437b1f6152d2f022bd/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/5cfcd4437b1f6152d2f022bd/pdb.gz): 203 ms

reading 510 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

510 atoms created

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

Time for creating model: 31 ms

Adding embedded #jmolscript: select ({0:509});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 basis of efficient coupling peptide ligation and ATP hydrolysis by gamma-gluatamylcysteine synthetase rcsb
molecule keywords	Glutamate--cysteine ligase
molecule tags	Ligase
source organism	Escherichia coli
total genus	188
structure length	510
sequence length	518
chains with identical sequence	B, C, D
ec nomenclature	ec 6.3.2.2: Glutamate--cysteine ligase.
pdb deposition date	2005-09-25

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF04262	Glu_cys_ligase	Glutamate-cysteine ligase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.590.20	Alpha Beta	2-Layer Sandwich	Creatine Kinase; Chain A, domain 2	Creatine Kinase; Chain A, domain 2	2d32A02

1V4GA 2D32A 2GWDA 1VA6A 2GWCA 3LN6A 3NZTA 3LN7A 1R8GA 2D33A 1TT4A
chains in the Genus database with same CATH superfamily

4AM1A 4BAXA 2D33A 1BG0A 3DRBA 3IG8A 1P50A 1QK1A 4LNNA 4GVZA 3B6RA 2J1QA 1R8GA 1TT4A 3L2EA 4RF6A 1HTQA 4GW2A 3FKYA 2BVCA 2CRKA 2WHIA 5J9AA 4LNFA 2D3CA 1P52A 4RF8A 1U6RA 3L2DA 2QC8A 2GLSA 1LGRA 3LVVA 1FPYA 3JQ3A 3LVWA 1F1HA 3DREA 1QH4A 3JPZA 3M10A 2D3AA 1RL9A 4XYCA 4BHLA 4RF7A 2GWDA 2GWCA 4LNIA 4BG4B 1VRPA 4GW0A 2D32A 1HTOA 2LGSA 1M15A 3NZTA 3JU5A 2UU7A 2D3BA 1VA6A 4Q2RA 4S0RA 1SD0A 3LN6A 5J99A 2OJWA 4ACFA 4LNKA 4S17A 4GVYA 3L2EB 3IG5A 3ZXVA 4BG4A 1V4GA 1CRKA 3ZXRA 4Z9MA 3JU6A 3NG0A 4RF9A 1G0WA 4HPPA 2WGSA 1F52A 4LNOA 1I0EA 3LN7A
chains in the Genus database with same CATH topology

2UU7A 2D3BA 1VA6A 3LVWA 4BAXA 3LN6A 2OJWA 2D33A 3FKYA 2D3AA 3IG5A 2D3CA 3IG8A 1V4GA 2GWDA 2GWCA 3NZTA 2QC8A 2D32A 3LVVA 3LN7A 1R8GA 1TT4A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 1V4G A;  2D32 A;  2GWD A;  1VA6 A;  2GWC A;  3LN6 A;  3NZT A;  3LN7 A;  1R8G A;  2D33 A;  1TT4 A; 
#chains in the Genus database with same CATH topology
 4AM1 A;  4BAX A;  2D33 A;  1BG0 A;  3DRB A;  3IG8 A;  1P50 A;  1QK1 A;  4LNN A;  4GVZ A;  3B6R A;  2J1Q A;  1R8G A;  1TT4 A;  3L2E A;  4RF6 A;  1HTQ A;  4GW2 A;  3FKY A;  2BVC A;  2CRK A;  2WHI A;  5J9A A;  4LNF A;  2D3C A;  1P52 A;  4RF8 A;  1U6R A;  3L2D A;  2QC8 A;  2GLS A;  1LGR A;  3LVV A;  1FPY A;  3JQ3 A;  3LVW A;  1F1H A;  3DRE A;  1QH4 A;  3JPZ A;  3M10 A;  2D3A A;  1RL9 A;  4XYC A;  4BHL A;  4RF7 A;  2GWD A;  2GWC A;  4LNI A;  4BG4 B;  1VRP A;  4GW0 A;  2D32 A;  1HTO A;  2LGS A;  1M15 A;  3NZT A;  3JU5 A;  2UU7 A;  2D3B A;  1VA6 A;  4Q2R A;  4S0R A;  1SD0 A;  3LN6 A;  5J99 A;  2OJW A;  4ACF A;  4LNK A;  4S17 A;  4GVY A;  3L2E B;  3IG5 A;  3ZXV A;  4BG4 A;  1V4G A;  1CRK A;  3ZXR A;  4Z9M A;  3JU6 A;  3NG0 A;  4RF9 A;  1G0W A;  4HPP A;  2WGS A;  1F52 A;  4LNO A;  1I0E A;  3LN7 A; 
#chains in the Genus database with same CATH homology
 2UU7 A;  2D3B A;  1VA6 A;  3LVW A;  4BAX A;  3LN6 A;  2OJW A;  2D33 A;  3FKY A;  2D3A A;  3IG5 A;  2D3C A;  3IG8 A;  1V4G A;  2GWD A;  2GWC A;  3NZT A;  2QC8 A;  2D32 A;  3LVV A;  3LN7 A;  1R8G A;  1TT4 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...

2D32A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations