5DIKA

Crystal structure of apo-lpg0406, a carboxymuconolactone decarboxylase family protein from legionella pneumophila
Total Genus 48
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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
48
sequence length
112
structure length
112
Chain Sequence
SDKFSHITKDITTQLAKFRKEMPELMTGFSSLAQAATKDGALDKKTKELIAMALAVAKQCPGCIGFHSQTLVKLQATREELLETLGMAVYMGGGPSLMYAAEALEAFEEFSK
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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.

Chord Diagram
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publication title Structure of lpg0406, a carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response from Legionella pneumophila
pubmed doi rcsb
molecule tags Oxidoreductase
source organism Legionella pneumophila
molecule keywords Alkyl hydroperoxide reductase AhpD
total genus 48
structure length 112
sequence length 112
chains with identical sequence B, C
ec nomenclature ec 1.11.1.15: Peroxiredoxin.
pdb deposition date 2015-09-01

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02627 CMD Carboxymuconolactone decarboxylase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.20.1290.10 Mainly Alpha Up-down Bundle AhpD-like AhpD-like 5dikA00
2O4DA 1ME5A 4G9QA 2OYOA 1LW1A 1GU9A 2IJCA 5DIKA 3LVYA 1VKEA 2AF7A 2Q0TA 2QEUA 2GMYA 3C1LA 5DIPA 2PRRA 1KNCA 1P8CA 3BEYA 2CWQA 3D7IA 2OUWA 2PFXA
chains in the Genus database with same CATH superfamily
2O4DA 1ME5A 4G9QA 3LK41 2KXPA 2OYOA 3AAEA 1LW1A 3AA1A 3AA6A 3LK2A 1GU9A 2IJCA 3AA0A 5DIKA 2ES9A 3AAAA 3LVYA 1VKEA 2AF7A 2Q0TA 2QEUA 2JN8A 4AKRA 2GMYA 5AFUK 2KZ7A 3C1LA 5DIPA 5ADXK 2PRRA 3AA7A 3LK3A 1IZNA 1KNCA 1P8CA 3BEYA 2CWQA 3D7IA 2OUWA 2PFXA
chains in the Genus database with same CATH topology
2O4DA 1ME5A 4G9QA 3LK41 2KXPA 2OYOA 3AAEA 1LW1A 3AA1A 3AA6A 3LK2A 1GU9A 2IJCA 3AA0A 5DIKA 2ES9A 3AAAA 3LVYA 1VKEA 2AF7A 2Q0TA 2QEUA 2JN8A 4AKRA 2GMYA 5AFUK 2KZ7A 3C1LA 5DIPA 5ADXK 2PRRA 3AA7A 3LK3A 1IZNA 1KNCA 1P8CA 3BEYA 2CWQA 3D7IA 2OUWA 2PFXA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2O4D A;  1ME5 A;  4G9Q A;  2OYO A;  1LW1 A;  1GU9 A;  2IJC A;  5DIK A;  3LVY A;  1VKE A;  2AF7 A;  2Q0T A;  2QEU A;  2GMY A;  3C1L A;  5DIP A;  2PRR A;  1KNC A;  1P8C A;  3BEY A;  2CWQ A;  3D7I A;  2OUW A;  2PFX A; 
#chains in the Genus database with same CATH topology
 2O4D A;  1ME5 A;  4G9Q A;  3LK4 1;  2KXP A;  2OYO A;  3AAE A;  1LW1 A;  3AA1 A;  3AA6 A;  3LK2 A;  1GU9 A;  2IJC A;  3AA0 A;  5DIK A;  2ES9 A;  3AAA A;  3LVY A;  1VKE A;  2AF7 A;  2Q0T A;  2QEU A;  2JN8 A;  4AKR A;  2GMY A;  5AFU K;  2KZ7 A;  3C1L A;  5DIP A;  5ADX K;  2PRR A;  3AA7 A;  3LK3 A;  1IZN A;  1KNC A;  1P8C A;  3BEY A;  2CWQ A;  3D7I A;  2OUW A;  2PFX A; 
#chains in the Genus database with same CATH homology
 2O4D A;  1ME5 A;  4G9Q A;  3LK4 1;  2KXP A;  2OYO A;  3AAE A;  1LW1 A;  3AA1 A;  3AA6 A;  3LK2 A;  1GU9 A;  2IJC A;  3AA0 A;  5DIK A;  2ES9 A;  3AAA A;  3LVY A;  1VKE A;  2AF7 A;  2Q0T A;  2QEU A;  2JN8 A;  4AKR A;  2GMY A;  5AFU K;  2KZ7 A;  3C1L A;  5DIP A;  5ADX K;  2PRR A;  3AA7 A;  3LK3 A;  1IZN A;  1KNC A;  1P8C A;  3BEY A;  2CWQ A;  3D7I A;  2OUW A;  2PFX 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)

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