5D2K | Genus

Total Genus 88

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	88
sequence length	263
structure length	263
Chain Sequence	NRTLTREQVLALAEHIENAELNVHDIGKVTNDFPEMTFADAYDVQWEIRRRKEARGNKIVGLKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEISVVTKAPLHGPGCHLGDVIAAIDYVIPTVEVIDSRYENFKFDPISVVADNASSTRFITGGRMASLEEVDLRTLGVVMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAERGEHIPAGTFIMTGGITAAVPVAPGDNITVRYQGLGSVSARFI

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__950518775488682__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__950518775488682__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/5D2K/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__950518775488682__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"950518775488682","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/5D2K/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__950518775488682__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d00e9b1442a1c6acfe3ddea/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d00e9b1442a1c6acfe3ddea/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d00e9b1442a1c6acfe3ddea/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/5d00e9b1442a1c6acfe3ddea/pdb.gz): 80 ms

reading 263 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

263 atoms created

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

Time for creating model: 28 ms

Adding embedded #jmolscript: select ({0:262});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 Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous beta-Keto Acid. pubmed doi rcsb
molecule keywords	4-oxalocrotonate decarboxylase NahK
molecule tags	Lyase
source organism	Pseudomonas putida
total genus	88
structure length	263
sequence length	263
chains with identical sequence	B
ec nomenclature	ec 4.1.1.77: 2-oxo-3-hexenedioate decarboxylase.
pdb deposition date	2015-08-05

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

cath code	Class	Architecture	Topology	Homology	Domain
3.90.850.10	Alpha Beta	Alpha-Beta Complex	Fumarylacetoacetate hydrolase; domain 2	Fumarylacetoacetase-like, C-terminal domain	5d2kA00

5D2JA 2Q1AX 1QQJA 3RR6A 2EB4A 1NR9A 2Q1CX 2Q1DX 1HYOA 4DBFA 1SV6A 1GTTA 2EB5A 1WZOA 3LZKA 5D2HA 3R6OA 4QKUA 5D2GA 3V77A 1I7OA 2Q18X 2DFUA 1NKQA 5D2IA 3BQBA 3QDFA 5D2KA 4DBHA 1QCOA 3S52A 4PFZA 1QCNA 2HZYA 5D2FA 2EB6A 2WQTA 4MAQA 1SAWA 2Q19X
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 5D2J A;  2Q1A X;  1QQJ A;  3RR6 A;  2EB4 A;  1NR9 A;  2Q1C X;  2Q1D X;  1HYO A;  4DBF A;  1SV6 A;  1GTT A;  2EB5 A;  1WZO A;  3LZK A;  5D2H A;  3R6O A;  4QKU A;  5D2G A;  3V77 A;  1I7O A;  2Q18 X;  2DFU A;  1NKQ A;  5D2I A;  3BQB A;  3QDF A;  5D2K A;  4DBH A;  1QCO A;  3S52 A;  4PFZ A;  1QCN A;  2HZY A;  5D2F A;  2EB6 A;  2WQT A;  4MAQ A;  1SAW A;  2Q19 X; 
#chains in the Genus database with same CATH topology
 5D2J A;  2Q1A X;  1QQJ A;  3RR6 A;  2EB4 A;  1NR9 A;  2Q1C X;  2Q1D X;  1HYO A;  4DBF A;  1SV6 A;  1GTT A;  2EB5 A;  1WZO A;  3LZK A;  5D2H A;  3R6O A;  4QKU A;  5D2G A;  3V77 A;  1I7O A;  2Q18 X;  2DFU A;  1NKQ A;  5D2I A;  3BQB A;  3QDF A;  5D2K A;  4DBH A;  1QCO A;  3S52 A;  4PFZ A;  1QCN A;  2HZY A;  5D2F A;  2EB6 A;  2WQT A;  4MAQ A;  1SAW A;  2Q19 X; 
#chains in the Genus database with same CATH homology
 5D2J A;  2Q1A X;  1QQJ A;  3RR6 A;  2EB4 A;  1NR9 A;  2Q1C X;  2Q1D X;  1HYO A;  4DBF A;  1SV6 A;  1GTT A;  2EB5 A;  1WZO A;  3LZK A;  5D2H A;  3R6O A;  4QKU A;  5D2G A;  3V77 A;  1I7O A;  2Q18 X;  2DFU A;  1NKQ A;  5D2I A;  3BQB A;  3QDF A;  5D2K A;  4DBH A;  1QCO A;  3S52 A;  4PFZ A;  1QCN A;  2HZY A;  5D2F A;  2EB6 A;  2WQT A;  4MAQ A;  1SAW A;  2Q19 X;

...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...

5D2KA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN