3LMX | Genus

Total Genus 42

Loading diagram...

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	42
sequence length	200
structure length	200
Chain Sequence	PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF

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__141035002621642__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__141035002621642__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3LMX/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__141035002621642__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"141035002621642","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3LMX/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__141035002621642__ ready

script 1 started

platformSpeed = 8

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	Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis rcsb
molecule keywords	Protocatechuate 3,4-dioxygenase alpha chain
molecule tags	Oxidoreductase
source organism	Pseudomonas putida
total genus	42
structure length	200
sequence length	200
chains with identical sequence	B, C
ec nomenclature	ec 1.13.11.3: Protocatechuate 3,4-dioxygenase.
pdb deposition date	2010-02-01

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00775	Dioxygenase_C	Dioxygenase

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	3lmxA00

3MI5A 3PCJA 2XSVA 3T67A 1DLMA 2BUMB 1TMXA 3O5UA 1EOCA 3PCLA 2BUWA 3PCGM 3O6JA 3HGIA 1EOBA 2PCDM 3MV6M 3PCGA 3I51A 3LKTM 2BURB 4WHOA 3T63M 2BUUA 1YKNA 3HHYA 2PCDA 3MFLM 2BUVA 3MV6A 3O32A 2BUYA 3LKTA 3PCEM 2BV0B 3PCFM 2XSUA 4WHSB 3MFLA 4WHOD 3TH1A 3LXVM 4WHRA 3PCEA 2BOYA 4WHQB 3HHXA 2BUXB 3LXVA 1YKMA 1EOCB 1EOAA 2BUMA 3O6RA 4ILTA 1YKOA 1DMHA 1DLTA 3PCBM 3MI1M 1YKKB 2BUQB 2BUZA 3PCMM 4WHPA 3T63A 4WHOB 1EO9B 2BUTB 2BUUB 3MI1A 3PCBA 1YKLA 3PCIM 3HJ8A 1YKPA 3PCFA 2BUYB 1EO2A 3PCLM 3PCHM 4WHPD 3HKPA 3PCIA 4WHSA 3LMXM 3PCAM 3PCNM 4WHRB 4WHRF 3PCHA 3N9TA 2BUWB 4WHQA 3LMXA 3PCAA 2XSRA 3PCNA 2BUXA 1YKMB 1EOAB 3I4YA 4WHSD 1EOBB 3PCCM 3HJSA 2BURA 3MV4A 1S9AA 1YKNB 3HJQA 3PCKM 1YKOB 3PCMA 2BUVB 1DLQA 4ILVA 2AZQA 3PCDM 2BUZB 1YKKA 3PCCA 4WHPB 3I4VA 2BUQA 3MV4M 2BV0A 3PCKA 3MI5M 1EO9A 1YKLB 2BUTA 3PCJM 3T67M 3PCDA 5TD3A 1YKPB 1EO2B
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 3MI5 A;  3PCJ A;  2XSV A;  3T67 A;  1DLM A;  2BUM B;  1TMX A;  3O5U A;  1EOC A;  3PCL A;  2BUW A;  3PCG M;  3O6J A;  3HGI A;  1EOB A;  2PCD M;  3MV6 M;  3PCG A;  3I51 A;  3LKT M;  2BUR B;  4WHO A;  3T63 M;  2BUU A;  1YKN A;  3HHY A;  2PCD A;  3MFL M;  2BUV A;  3MV6 A;  3O32 A;  2BUY A;  3LKT A;  3PCE M;  2BV0 B;  3PCF M;  2XSU A;  4WHS B;  3MFL A;  4WHO D;  3TH1 A;  3LXV M;  4WHR A;  3PCE A;  2BOY A;  4WHQ B;  3HHX A;  2BUX B;  3LXV A;  1YKM A;  1EOC B;  1EOA A;  2BUM A;  3O6R A;  4ILT A;  1YKO A;  1DMH A;  1DLT A;  3PCB M;  3MI1 M;  1YKK B;  2BUQ B;  2BUZ A;  3PCM M;  4WHP A;  3T63 A;  4WHO B;  1EO9 B;  2BUT B;  2BUU B;  3MI1 A;  3PCB A;  1YKL A;  3PCI M;  3HJ8 A;  1YKP A;  3PCF A;  2BUY B;  1EO2 A;  3PCL M;  3PCH M;  4WHP D;  3HKP A;  3PCI A;  4WHS A;  3LMX M;  3PCA M;  3PCN M;  4WHR B;  4WHR F;  3PCH A;  3N9T A;  2BUW B;  4WHQ A;  3LMX A;  3PCA A;  2XSR A;  3PCN A;  2BUX A;  1YKM B;  1EOA B;  3I4Y A;  4WHS D;  1EOB B;  3PCC M;  3HJS A;  2BUR A;  3MV4 A;  1S9A A;  1YKN B;  3HJQ A;  3PCK M;  1YKO B;  3PCM A;  2BUV B;  1DLQ A;  4ILV A;  2AZQ A;  3PCD M;  2BUZ B;  1YKK A;  3PCC A;  4WHP B;  3I4V A;  2BUQ A;  3MV4 M;  2BV0 A;  3PCK A;  3MI5 M;  1EO9 A;  1YKL B;  2BUT A;  3PCJ M;  3T67 M;  3PCD A;  5TD3 A;  1YKP B;  1EO2 B; 
#chains in the Genus database with same CATH topology
 3MI5 A;  3PCJ A;  2XSV A;  3T67 A;  1DLM A;  2BUM B;  1TMX A;  3O5U A;  1EOC A;  3PCL A;  2BUW A;  3PCG M;  3O6J A;  3HGI A;  1EOB A;  2PCD M;  3MV6 M;  3PCG A;  3I51 A;  3LKT M;  2BUR B;  4WHO A;  3T63 M;  2BUU A;  1YKN A;  3HHY A;  2PCD A;  3MFL M;  2BUV A;  3MV6 A;  3O32 A;  2BUY A;  3LKT A;  3PCE M;  2BV0 B;  3PCF M;  2XSU A;  4WHS B;  3MFL A;  4WHO D;  3TH1 A;  3LXV M;  4WHR A;  3PCE A;  2BOY A;  4WHQ B;  3HHX A;  2BUX B;  3LXV A;  1YKM A;  1EOC B;  1EOA A;  2BUM A;  3O6R A;  4ILT A;  1YKO A;  1DMH A;  1DLT A;  3PCB M;  3MI1 M;  1YKK B;  2BUQ B;  2BUZ A;  3PCM M;  4WHP A;  3T63 A;  4WHO B;  1EO9 B;  2BUT B;  2BUU B;  3MI1 A;  3PCB A;  1YKL A;  3PCI M;  3HJ8 A;  1YKP A;  3PCF A;  2BUY B;  1EO2 A;  3PCL M;  3PCH M;  4WHP D;  3HKP A;  3PCI A;  4WHS A;  3LMX M;  3PCA M;  3PCN M;  4WHR B;  4WHR F;  3PCH A;  3N9T A;  2BUW B;  4WHQ A;  3LMX A;  3PCA A;  2XSR A;  3PCN A;  2BUX A;  1YKM B;  1EOA B;  3I4Y A;  4WHS D;  1EOB B;  3PCC M;  3HJS A;  2BUR A;  3MV4 A;  1S9A A;  1YKN B;  3HJQ A;  3PCK M;  1YKO B;  3PCM A;  2BUV B;  1DLQ A;  4ILV A;  2AZQ A;  3PCD M;  2BUZ B;  1YKK A;  3PCC A;  4WHP B;  3I4V A;  2BUQ A;  3MV4 M;  2BV0 A;  3PCK A;  3MI5 M;  1EO9 A;  1YKL B;  2BUT A;  3PCJ M;  3T67 M;  3PCD A;  5TD3 A;  1YKP B;  1EO2 B; 
#chains in the Genus database with same CATH homology
 3MI5 A;  3PCJ A;  2XSV A;  3T67 A;  1DLM A;  2BUM B;  1TMX A;  3O5U A;  1EOC A;  3PCL A;  2BUW A;  3PCG M;  3O6J A;  3HGI A;  1EOB A;  2PCD M;  3MV6 M;  3PCG A;  3I51 A;  3LKT M;  2BUR B;  4WHO A;  3T63 M;  2BUU A;  1YKN A;  3HHY A;  2PCD A;  3MFL M;  2BUV A;  3MV6 A;  3O32 A;  2BUY A;  3LKT A;  3PCE M;  2BV0 B;  3PCF M;  2XSU A;  4WHS B;  3MFL A;  4WHO D;  3TH1 A;  3LXV M;  4WHR A;  3PCE A;  2BOY A;  4WHQ B;  3HHX A;  2BUX B;  3LXV A;  1YKM A;  1EOC B;  1EOA A;  2BUM A;  3O6R A;  4ILT A;  1YKO A;  1DMH A;  1DLT A;  3PCB M;  3MI1 M;  1YKK B;  2BUQ B;  2BUZ A;  3PCM M;  4WHP A;  3T63 A;  4WHO B;  1EO9 B;  2BUT B;  2BUU B;  3MI1 A;  3PCB A;  1YKL A;  3PCI M;  3HJ8 A;  1YKP A;  3PCF A;  2BUY B;  1EO2 A;  3PCL M;  3PCH M;  4WHP D;  3HKP A;  3PCI A;  4WHS A;  3LMX M;  3PCA M;  3PCN M;  4WHR B;  4WHR F;  3PCH A;  3N9T A;  2BUW B;  4WHQ A;  3LMX A;  3PCA A;  2XSR A;  3PCN A;  2BUX A;  1YKM B;  1EOA B;  3I4Y A;  4WHS D;  1EOB B;  3PCC M;  3HJS A;  2BUR A;  3MV4 A;  1S9A A;  1YKN B;  3HJQ A;  3PCK M;  1YKO B;  3PCM A;  2BUV B;  1DLQ A;  4ILV A;  2AZQ A;  3PCD M;  2BUZ B;  1YKK A;  3PCC A;  4WHP B;  3I4V A;  2BUQ A;  3MV4 M;  2BV0 A;  3PCK A;  3MI5 M;  1EO9 A;  1YKL B;  2BUT A;  3PCJ M;  3T67 M;  3PCD A;  5TD3 A;  1YKP B;  1EO2 B;

...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...

3LMXA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations