3PCB | Genus

Total Genus 57

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	57
sequence length	236
structure length	233
Chain Sequence	PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFE

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__120342711661063__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__120342711661063__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3PCB/M/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__120342711661063__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"120342711661063","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3PCB/M/"

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__120342711661063__ 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

publication title	Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site. pubmed doi rcsb
molecule keywords	PROTOCATECHUATE 3,4-DIOXYGENASE
molecule tags	Dioxygenase
total genus	57
structure length	233
sequence length	236
chains with identical sequence	N, O, P, Q, R
ec nomenclature	ec 1.13.11.3: Protocatechuate 3,4-dioxygenase.
pdb deposition date	1997-04-25

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
M	PF00775	Dioxygenase_C	Dioxygenase
M	PF12391	PCDO_beta_N	Protocatechuate 3,4-dioxygenase beta subunit N terminal

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	3pcbM00

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

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

3PCBM

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations