1YKOB

Protocatechuate 3,4-dioxygenase y408h mutant
Total Genus 50
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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
50
sequence length
238
structure length
237
Chain Sequence
PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRHRHKNDRYLAPLDPNFGGVGRLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC
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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

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

molecule tags Oxidoreductase
molecule keywords Protocatechuate 3,4-dioxygenase alpha chain
publication title Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis
pubmed doi rcsb
source organism Pseudomonas putida
total genus 50
structure length 237
sequence length 238
chains with identical sequence D, F, H, J, L
ec nomenclature ec 1.13.11.3: Protocatechuate 3,4-dioxygenase.
pdb deposition date 2005-01-18

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF00775 Dioxygenase_C Dioxygenase
B PF12391 PCDO_beta_N Protocatechuate 3,4-dioxygenase beta subunit N terminal
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.60.130.10 Mainly Beta Sandwich Protocatechuate 3,4-Dioxygenase, subunit A Aromatic compound dioxygenase 1ykoB00
3O6RA 3PCLA 1EO9B 2BUQA 3O32A 3PCLM 2BUYB 3HJSA 3PCEA 3O6JA 2BUXA 3PCEM 2BV0A 4WHPA 3TH1A 4WHQB 2XSUA 4WHOA 3T63A 3MI1A 1EOBA 3T63M 3I51A 3PCIA 1EOCA 3MI1M 2BUQB 1EO2A 3PCAA 3T67A 2BUMB 3PCIM 3HHXA 4WHPD 4WHRA 3T67M 3PCAM 3PCKA 3MFLA 1EOAB 3LMXM 3PCBA 4WHOD 3PCKM 3MFLM 4WHPB 3HKPA 3PCJA 3PCBM 1YKPA 2BUUB 1DLQA 4WHSA 1YKLA 2BOYA 2BUWA 3PCJM 3PCNA 1YKNA 4WHOB 1YKKB 2PCDA 1YKOA 3PCNM 3I4VA 3LKTA 2PCDM 1YKMA 2BUVA 3LKTM 1EO2B 2BURA 1DLTA 3PCMA 4WHSD 3MI5A 3PCMM 4WHRF 4ILVA 3LMXA 5TD3A 3MI5M 1DLMA 2BUWB 2BUXB 3PCFA 2BV0B 3HHYA 2BUYA 3PCFM 3HJ8A 3N9TA 3LXVA 2BUVB 3LXVM 3PCHA 1TMXA 3MV6A 1EOBB 3MV4A 3PCHM 1EOCB 3MV6M 3MV4M 4WHRB 2BUTA 2BUZA 3PCGA 1DMHA 3PCCA 2BUMA 2XSRA 3PCGM 1YKPB 3PCCM 3HJQA 1EO9A 1EOAA 1YKLB 4WHSB 1YKNB 3PCDA 1YKOB 2BUUA 3PCDM 2XSVA 1YKMB 1YKKA 3HGIA 3O5UA 2BURB 4WHQA 1S9AA 3I4YA 2BUTB 2AZQA 2BUZB 4ILTA
chains in the Genus database with same CATH superfamily
3O6RA 3PCLA 1EO9B 2BUQA 3O32A 3PCLM 2BUYB 3HJSA 3PCEA 3O6JA 2BUXA 3PCEM 2BV0A 4WHPA 3TH1A 4WHQB 2XSUA 4WHOA 3T63A 3MI1A 1EOBA 3T63M 3I51A 3PCIA 1EOCA 3MI1M 2BUQB 1EO2A 3PCAA 3T67A 2BUMB 3PCIM 3HHXA 4WHPD 4WHRA 3T67M 3PCAM 3PCKA 3MFLA 1EOAB 3LMXM 3PCBA 4WHOD 3PCKM 3MFLM 4WHPB 3HKPA 3PCJA 3PCBM 1YKPA 2BUUB 1DLQA 4WHSA 1YKLA 2BOYA 2BUWA 3PCJM 3PCNA 1YKNA 4WHOB 1YKKB 2PCDA 1YKOA 3PCNM 3I4VA 3LKTA 2PCDM 1YKMA 2BUVA 3LKTM 1EO2B 2BURA 1DLTA 3PCMA 4WHSD 3MI5A 3PCMM 4WHRF 4ILVA 3LMXA 5TD3A 3MI5M 1DLMA 2BUWB 2BUXB 3PCFA 2BV0B 3HHYA 2BUYA 3PCFM 3HJ8A 3N9TA 3LXVA 2BUVB 3LXVM 3PCHA 1TMXA 3MV6A 1EOBB 3MV4A 3PCHM 1EOCB 3MV6M 3MV4M 4WHRB 2BUTA 2BUZA 3PCGA 1DMHA 3PCCA 2BUMA 2XSRA 3PCGM 1YKPB 3PCCM 3HJQA 1EO9A 1EOAA 1YKLB 4WHSB 1YKNB 3PCDA 1YKOB 2BUUA 3PCDM 2XSVA 1YKMB 1YKKA 3HGIA 3O5UA 2BURB 4WHQA 1S9AA 3I4YA 2BUTB 2AZQA 2BUZB 4ILTA
chains in the Genus database with same CATH topology
3O6RA 3PCLA 1EO9B 2BUQA 3O32A 3PCLM 2BUYB 3HJSA 3PCEA 3O6JA 2BUXA 3PCEM 2BV0A 4WHPA 3TH1A 4WHQB 2XSUA 4WHOA 3T63A 3MI1A 1EOBA 3T63M 3I51A 3PCIA 1EOCA 3MI1M 2BUQB 1EO2A 3PCAA 3T67A 2BUMB 3PCIM 3HHXA 4WHPD 4WHRA 3T67M 3PCAM 3PCKA 3MFLA 1EOAB 3LMXM 3PCBA 4WHOD 3PCKM 3MFLM 4WHPB 3HKPA 3PCJA 3PCBM 1YKPA 2BUUB 1DLQA 4WHSA 1YKLA 2BOYA 2BUWA 3PCJM 3PCNA 1YKNA 4WHOB 1YKKB 2PCDA 1YKOA 3PCNM 3I4VA 3LKTA 2PCDM 1YKMA 2BUVA 3LKTM 1EO2B 2BURA 1DLTA 3PCMA 4WHSD 3MI5A 3PCMM 4WHRF 4ILVA 3LMXA 5TD3A 3MI5M 1DLMA 2BUWB 2BUXB 3PCFA 2BV0B 3HHYA 2BUYA 3PCFM 3HJ8A 3N9TA 3LXVA 2BUVB 3LXVM 3PCHA 1TMXA 3MV6A 1EOBB 3MV4A 3PCHM 1EOCB 3MV6M 3MV4M 4WHRB 2BUTA 2BUZA 3PCGA 1DMHA 3PCCA 2BUMA 2XSRA 3PCGM 1YKPB 3PCCM 3HJQA 1EO9A 1EOAA 1YKLB 4WHSB 1YKNB 3PCDA 1YKOB 2BUUA 3PCDM 2XSVA 1YKMB 1YKKA 3HGIA 3O5UA 2BURB 4WHQA 1S9AA 3I4YA 2BUTB 2AZQA 2BUZB 4ILTA
chains in the Genus database with same CATH homology


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

 
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