1OGDA

The structure of bacillus subtilis rbsd complexed with d-ribose
Slipknot S +31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 21-113 93 1-20 123-131 114-122 20 9 slipknot
Chain Sequence
MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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2.1 7-112 106 1-6 117-131 113-116 6 15 slipknot
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3.1 12-113 102 1-11 120-131 114-119 11 12 slipknot
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2.1 12-119 108 1-11 123-131 120-122 11 9 slipknot
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2.1 11-122 112 1-3, 125-131 4-10, 123-124 3 7 slipknot
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2.1 17-112 96 1-9, 117-131 10-16, 113-116 9 15 slipknot
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3.1 25-113 89 1-11, 122-131 12-24, 114-121 11 10 slipknot
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2.1 25-121 97 1-11, 123-131 12-24, 122-122 11 9 slipknot
sequence length 131
structure length 131
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 Genus: 37
ec nomenclature ec 5.4.99.62: D-ribose pyranase.
pdb deposition date 2003-04-30
KnotProt deposition date 2014-07-31

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 1ogdA01
2OB5A 1OGFA 1OGDA 4A34A 3P13A 2WCUA 3P12A 2WCVA 1OGEA 3MVKA 1OGCA 3E7NA
chains in the KnotProt database with same CATH superfamily
2OB5A 1OGFA 1OGDA 4A34A 3P13A 2WCUA 3P12A 2WCVA 1OGEA 3MVKA 1OGCA 3E7NA
chains in the KnotProt database with same CATH topology
2OB5A 1OGFA 1OGDA 4A34A 3P13A 2WCUA 3P12A 2WCVA 1OGEA 3MVKA 1OGCA 3E7NA
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 2OB5 A;  1OGF A;  1OGD A;  4A34 A;  3P13 A;  2WCU A;  3P12 A;  2WCV A;  1OGE A;  3MVK A;  1OGC A;  3E7N A; 
#chains in the KnotProt database with same CATH topology
 2OB5 A;  1OGF A;  1OGD A;  4A34 A;  3P13 A;  2WCU A;  3P12 A;  2WCV A;  1OGE A;  3MVK A;  1OGC A;  3E7N A; 
#chains in the KnotProt database with same CATH homology
 2OB5 A;  1OGF A;  1OGD A;  4A34 A;  3P13 A;  2WCU A;  3P12 A;  2WCV A;  1OGE A;  3MVK A;  1OGC A;  3E7N A; 
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the KnotProt 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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