1GTT | Genus

Total Genus 123

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	123
sequence length	429
structure length	421
Chain Sequence	MKGTIFAVALNHRSQLDAWQEAFQQSPYKAPPKTAVWFIKPRNTVIGCGEPIPFPQGEKVLSGATVALIVGKTATKVREEDAAEYIAGYALANDVSLPEESFYRPAIKAKCRDGFCPIGETVALSNVDNLTIYTEINGRPADHWNTADLQRNAAQLLSALSEFATLNPGDAILLGTPQARVEIQPGDRVRVLAEGFPPLENPVVDEREVTTRKSFPTLPHPHGTLFALGLNYADHPEEPLVFLKAPNTLTGDNQTSVRPNNIEYMHYEAELVVVIGKQARNVSEADAMDYVAGYTVCNDYAIRDYLENYYRPNLRVKSRDGLTPMLSTIVPKEAIPDPHNLTLRTFVNGELRQQGTTADLIFSVPFLIAYLSEFMTLNPGDMIATGTPKGLSDVVPGDEVVVEVEGVGRLVNRIVSEETAK

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__206078088795098__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__206078088795098__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1GTT/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__206078088795098__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"206078088795098","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1GTT/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__206078088795098__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfb40f6b3924d457152fee3/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfb40f6b3924d457152fee3/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfb40f6b3924d457152fee3/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/5cfb40f6b3924d457152fee3/pdb.gz): 415 ms

reading 421 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

421 atoms created

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

Time for creating model: 29 ms

Adding embedded #jmolscript: select ({0:420});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

molecule tags	Isomerase
source organism	Escherichia coli
publication title	The Crystal Structure of Hpce, a Bifunctional Decarboxylase/Isomerase with a Multifunctional Fold. pubmed doi rcsb
molecule keywords	4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DE
total genus	123
structure length	421
sequence length	429
chains with identical sequence	B, C, D
ec nomenclature	ec 4.1.1.68: 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase.
pdb deposition date	2002-01-18

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01557	FAA_hydrolase	Fumarylacetoacetate (FAA) hydrolase family

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	1gttA01
3.90.850.10	Alpha Beta	Alpha-Beta Complex	Fumarylacetoacetate hydrolase; domain 2	Fumarylacetoacetase-like, C-terminal domain	1gttA02

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

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

1GTTA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations