1OGCA

The structure of bacillus subtilis rbsd complexed with d-ribose
Total Genus 34
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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
34
Knots found
sequence length
131
structure length
131
Chain Sequence
MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF
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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 Crystal Structures of Rbsd Leading to the Identification of Cytoplasmic Sugar-Binding Proteins with a Novel Folding Architecture
pubmed doi rcsb
molecule tags Transport
molecule keywords HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
total genus 34
structure length 131
sequence length 131
chains with identical sequence B, C, D, E
other databases KnotProt 2.0: S +31
ec nomenclature ec 5.4.99.62: D-ribose pyranase.
pdb deposition date 2003-04-30

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF05025 RbsD_FucU RbsD / FucU transport protein family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1650.10 Alpha Beta 3-Layer(aba) Sandwich RbsD-like fold RbsD-like domain 1ogcA01
4A34A 1OGFA 3E7NA 3P13A 2WCUA 1OGEA 2WCVA 1OGDA 3MVKA 2OB5A 1OGCA 3P12A
chains in the Genus database with same CATH superfamily
4A34A 1OGFA 3E7NA 3P13A 2WCUA 1OGEA 2WCVA 1OGDA 3MVKA 2OB5A 1OGCA 3P12A
chains in the Genus database with same CATH topology
4A34A 1OGFA 3E7NA 3P13A 2WCUA 1OGEA 2WCVA 1OGDA 3MVKA 2OB5A 1OGCA 3P12A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4A34 A;  1OGF A;  3E7N A;  3P13 A;  2WCU A;  1OGE A;  2WCV A;  1OGD A;  3MVK A;  2OB5 A;  1OGC A;  3P12 A; 
#chains in the Genus database with same CATH topology
 4A34 A;  1OGF A;  3E7N A;  3P13 A;  2WCU A;  1OGE A;  2WCV A;  1OGD A;  3MVK A;  2OB5 A;  1OGC A;  3P12 A; 
#chains in the Genus database with same CATH homology
 4A34 A;  1OGF A;  3E7N A;  3P13 A;  2WCU A;  1OGE A;  2WCV A;  1OGD A;  3MVK A;  2OB5 A;  1OGC A;  3P12 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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