1YKPA

Protocatechuate 3,4-dioxygenase y408h mutant bound to dhb
Total Genus 42
204060801001201401601800510152025303540
Genus TraceResidueGenus

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

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.

Chord Diagram
EMPTYTI1 (14-17)S9 (126-132)AH1 (17-21)TVIII1 (31-34)S5 (92-96)TVIII2 (87-90)TI2 (41-44)TI5 (84-87)S1 (48-53)S2 (55-56)TIV1 (63-66)S13 (187-188)TI3 (57-60)TIV2 (98-101)TII1 (132-135)S3 (66-74)S4 (78-79)S6 (104-109)S12 (180-184)TVIII3 (101-104)S7 (114-115)S8 (121-122)TI6 (116-119)S10 (135-145)TI8 (155-158)3H3 (168-170)S11 (171-177)TI7 (145-148)AH2 (149-154)3H2 (158-160)AH3 (164-167)TII2 (191-194)TI4 (74-77)3H1 (24-26)Updating...
connected with : NaN
publication title Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis
pubmed doi rcsb
molecule tags Oxidoreductase
source organism Pseudomonas putida
molecule keywords Protocatechuate 3,4-dioxygenase alpha chain
total genus 42
structure length 200
sequence length 200
chains with identical sequence C, E, G, I, K
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
A PF00775 Dioxygenase_C Dioxygenase
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 1ykpA00
1EO9B 3PCMM 1YKMB 1YKKA 2BUWB 1EOAB 3N9TA 4WHPA 2BUUA 4WHRA 2AZQA 4WHOB 2BUYA 3PCLA 1EOBA 3PCGA 1DLQA 2BUZA 3PCGM 3HJQA 1YKKB 2PCDA 4WHPB 2PCDM 3PCJM 3O6JA 4WHRB 1TMXA 2BUYB 3PCEA 2BUQA 1EOBB 4WHSD 2BUZB 3PCEM 2XSUA 1EOCA 4ILTA 2BUXA 2BUVA 3PCCA 2XSRA 3PCKA 3PCCM 2BUQB 3PCKM 4WHQA 3PCLM 3LMXA 1YKOB 3HGIA 3T67A 3LMXM 1EOCB 1S9AA 2BUMB 2BUXB 3T67M 2BUVB 3MI5A 1DLTA 3TH1A 3I51A 3O6RA 3MI5M 3HJSA 2BURA 3PCBA 3MFLA 1YKOA 1YKNB 1EO2A 4WHQB 4ILVA 3PCBM 3MFLM 4WHOD 2BUMA 3I4YA 3MV4A 3I4VA 1YKLB 1DMHA 3MV4M 3PCHA 2BUTB 2BV0A 3LKTA 2BURB 1YKNA 4WHPD 4WHSA 3LKTM 3MI1A 3LXVA 1EO2B 3PCIA 1YKLA 3O32A 3PCIM 2BUTA 2XSVA 1YKPA 3HHYA 2BV0B 3PCAA 3PCDA 4WHSB 3PCAM 5TD3A 3PCDM 3O5UA 3PCNA 3HJ8A 1EO9A 3PCNM 3MV6A 1YKMA 3PCFA 2BUWA 3PCHM 1EOAA 1YKPB 3MV6M 3T63A 3PCFM 2BOYA 1DLMA 3PCJA 3HKPA 3T63M 2BUUB 4WHOA 4WHRF 3HHXA 3MI1M 3LXVM 3PCMA
chains in the Genus database with same CATH superfamily
1EO9B 3PCMM 1YKMB 1YKKA 2BUWB 1EOAB 3N9TA 4WHPA 2BUUA 4WHRA 2AZQA 4WHOB 2BUYA 3PCLA 1EOBA 3PCGA 1DLQA 2BUZA 3PCGM 3HJQA 1YKKB 2PCDA 4WHPB 2PCDM 3PCJM 3O6JA 4WHRB 1TMXA 2BUYB 3PCEA 2BUQA 1EOBB 4WHSD 2BUZB 3PCEM 2XSUA 1EOCA 4ILTA 2BUXA 2BUVA 3PCCA 2XSRA 3PCKA 3PCCM 2BUQB 3PCKM 4WHQA 3PCLM 3LMXA 1YKOB 3HGIA 3T67A 3LMXM 1EOCB 1S9AA 2BUMB 2BUXB 3T67M 2BUVB 3MI5A 1DLTA 3TH1A 3I51A 3O6RA 3MI5M 3HJSA 2BURA 3PCBA 3MFLA 1YKOA 1YKNB 1EO2A 4WHQB 4ILVA 3PCBM 3MFLM 4WHOD 2BUMA 3I4YA 3MV4A 3I4VA 1YKLB 1DMHA 3MV4M 3PCHA 2BUTB 2BV0A 3LKTA 2BURB 1YKNA 4WHPD 4WHSA 3LKTM 3MI1A 3LXVA 1EO2B 3PCIA 1YKLA 3O32A 3PCIM 2BUTA 2XSVA 1YKPA 3HHYA 2BV0B 3PCAA 3PCDA 4WHSB 3PCAM 5TD3A 3PCDM 3O5UA 3PCNA 3HJ8A 1EO9A 3PCNM 3MV6A 1YKMA 3PCFA 2BUWA 3PCHM 1EOAA 1YKPB 3MV6M 3T63A 3PCFM 2BOYA 1DLMA 3PCJA 3HKPA 3T63M 2BUUB 4WHOA 4WHRF 3HHXA 3MI1M 3LXVM 3PCMA
chains in the Genus database with same CATH topology
1EO9B 3PCMM 1YKMB 1YKKA 2BUWB 1EOAB 3N9TA 4WHPA 2BUUA 4WHRA 2AZQA 4WHOB 2BUYA 3PCLA 1EOBA 3PCGA 1DLQA 2BUZA 3PCGM 3HJQA 1YKKB 2PCDA 4WHPB 2PCDM 3PCJM 3O6JA 4WHRB 1TMXA 2BUYB 3PCEA 2BUQA 1EOBB 4WHSD 2BUZB 3PCEM 2XSUA 1EOCA 4ILTA 2BUXA 2BUVA 3PCCA 2XSRA 3PCKA 3PCCM 2BUQB 3PCKM 4WHQA 3PCLM 3LMXA 1YKOB 3HGIA 3T67A 3LMXM 1EOCB 1S9AA 2BUMB 2BUXB 3T67M 2BUVB 3MI5A 1DLTA 3TH1A 3I51A 3O6RA 3MI5M 3HJSA 2BURA 3PCBA 3MFLA 1YKOA 1YKNB 1EO2A 4WHQB 4ILVA 3PCBM 3MFLM 4WHOD 2BUMA 3I4YA 3MV4A 3I4VA 1YKLB 1DMHA 3MV4M 3PCHA 2BUTB 2BV0A 3LKTA 2BURB 1YKNA 4WHPD 4WHSA 3LKTM 3MI1A 3LXVA 1EO2B 3PCIA 1YKLA 3O32A 3PCIM 2BUTA 2XSVA 1YKPA 3HHYA 2BV0B 3PCAA 3PCDA 4WHSB 3PCAM 5TD3A 3PCDM 3O5UA 3PCNA 3HJ8A 1EO9A 3PCNM 3MV6A 1YKMA 3PCFA 2BUWA 3PCHM 1EOAA 1YKPB 3MV6M 3T63A 3PCFM 2BOYA 1DLMA 3PCJA 3HKPA 3T63M 2BUUB 4WHOA 4WHRF 3HHXA 3MI1M 3LXVM 3PCMA
chains in the Genus database with same CATH homology


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