5M1EA

Crystal structure of n-terminally tagged ubid from e. coli reconstituted with prfmn cofactor
Total Genus 144
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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
144
sequence length
487
structure length
469
Chain Sequence
YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKKQVLNMPTKRLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIFN
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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 Lyase
molecule keywords 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
publication title Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis.
pubmed doi rcsb
source organism Escherichia coli o6:h1 (strain cft073 / atcc 700928 / upec)
total genus 144
structure length 469
sequence length 487
chains with identical sequence B, C
ec nomenclature ec 4.1.1.98: 4-hydroxy-3-polyprenylbenzoate decarboxylase.
pdb deposition date 2016-10-07

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01977 UbiD 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1670.10 Alpha Beta 3-Layer(aba) Sandwich UbiD C-terminal domain-like UbiD C-terminal domain-like 5m1eA02
5M1BA 2IDBA 5M1EA 5M1CA 5M1DA 4IP2A 4IWSA
chains in the Genus database with same CATH superfamily
5M1BA 2IDBA 5M1EA 5M1CA 5M1DA 4IP2A 4IWSA
chains in the Genus database with same CATH topology
5M1BA 2IDBA 5M1EA 5M1CA 5M1DA 4IP2A 4IWSA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5M1B A;  2IDB A;  5M1E A;  5M1C A;  5M1D A;  4IP2 A;  4IWS A; 
#chains in the Genus database with same CATH topology
 5M1B A;  2IDB A;  5M1E A;  5M1C A;  5M1D A;  4IP2 A;  4IWS A; 
#chains in the Genus database with same CATH homology
 5M1B A;  2IDB A;  5M1E A;  5M1C A;  5M1D A;  4IP2 A;  4IWS 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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#similar chains in the pdb database (?% sequence similarity)
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