3PCD | Genus

Total Genus 56

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	56
sequence length	236
structure length	233
Chain Sequence	PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPHPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFE

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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

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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	The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates. pubmed doi rcsb
molecule keywords	PROTOCATECHUATE 3,4-DIOXYGENASE
molecule tags	Dioxygenase
source organism	Pseudomonas putida
total genus	56
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	1997-11-24

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	3pcdM00

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

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

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similar chains in the Genus database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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3PCDM

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations