4GVY | Genus

Total Genus 129

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	129
sequence length	356
structure length	356
Chain Sequence	VDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKQWGDINTLVGLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA

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__0105422689293753__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__0105422689293753__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4GVY/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__0105422689293753__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"0105422689293753","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4GVY/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__0105422689293753__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0031ec80cc945713e3fb5e/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0031ec80cc945713e3fb5e/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0031ec80cc945713e3fb5e/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/5d0031ec80cc945713e3fb5e/pdb.gz): 63 ms

reading 356 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

356 atoms created

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

Time for creating model: 24 ms

Adding embedded #jmolscript: select ({0:355});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	Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. pubmed doi rcsb
molecule keywords	Arginine kinase
molecule tags	Transferase
source organism	Limulus polyphemus
total genus	129
structure length	356
sequence length	356
ec nomenclature	ec 2.7.3.3: Arginine kinase.
pdb deposition date	2012-08-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00217	ATP-gua_Ptrans	ATP:guanido phosphotransferase, C-terminal catalytic domain
A	PF02807	ATP-gua_PtransN	ATP:guanido phosphotransferase, N-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.135.10	Mainly Alpha	Orthogonal Bundle	Transferase Creatine Kinase; Chain A, domain 1	ATP:guanido phosphotransferase, N-terminal domain	4gvyA01
3.30.590.10	Alpha Beta	2-Layer Sandwich	Creatine Kinase; Chain A, domain 2	Glutamine synthetase/guanido kinase, catalytic domain	4gvyA02

3L2DA 4BG4B 4S17A 4RF6A 4BHLA 4Z9MA 3B6RA 1FPYA 4GW0A 4GW2A 4RF8A 1HTQA 3JU5A 1QH4A 4GVYA 3M10A 1BG0A 4LNKA 4GVZA 2WGSA 3DRBA 1RL9A 3NG0A 1QK1A 4XYCA 3L2EA 5J9AA 4LNIA 4LNOA 4LNFA 2LGSA 1M15A 1I0EA 4HPPA 3JPZA 1VRPA 4AM1A 1F1HA 1SD0A 4Q2RA 4RF9A 2WHIA 4BG4A 1U6RA 2GLSA 3DREA 3ZXRA 3L2EB 3ZXVA 4ACFA 3JU6A 2BVCA 3JQ3A 2J1QA 5J99A 1LGRA 1G0WA 1CRKA 4RF7A 1F52A 4LNNA 4S0RA 1P50A 1HTOA 1P52A 2CRKA
chains in the Genus database with same CATH superfamily

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

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

4GVYA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations