5BU6B

Structure of bpsb deaceylase domain from bordetella bronchiseptica
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
view details
+31 8-262 255 263-264 1-1 2-7 1 1 slipknot
Chain Sequence
PDPDDGLTFRVLSMHDVRDNLRASFADMPDQFAIETRTLTDLFEWIRVKGFNPISMQQIIDSRAGVRPLPPRPILLTFDDGYASTYTKVFPLLAAFNYPAVVAVVTSWTDAPAGTKIRLSPKIEVPHDFFMTWAQLREMAQSGLVELASHSHNLHRGVLANPQGNEQPAASSRQYLPASGRYENDAEYRARVRQDLKTSAHLIRHHTGVTIRSIVWPYGAHNRDTDQVAAEVGLNIGLTLQPGPNTPDVALTQIRRSLVDYEVN
Note, that the numbers in the matrix denote the consecutive residues in the loop, not the index of amino acids in the chain!
Knot K 3x +31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
+ 31 12-192 181 1-11, 193-196 11 4 knot
Fingerprint Knot forming loop Loop type
K +31 Pro35 ... Asp114 <->
Bridging ionNi401
<-> His184 ...
Chain closureAsn298 <-> Pro35
probabilistic
K +31
Chain closurePro35 <-> Asn298
... His189 <->
Bridging ionNi401
<-> His184 ... Pro35
probabilistic
K +31 Pro35 ... Asp114 <->
Bridging ionNi401
<-> His189 ...
Chain closureAsn298 <-> Pro35
probabilistic
Chain Sequence
PDPDDGLTFRVLSMHDVRDNLRASFADMPDQFAIETRTLTDLFEWIRVKGFNPISMQQIIDSRAGVRPLPPRPILLTFDDGYASTYTKVFPLLAAFNYPAVVAVVTSWTDAPAGTKIRLSPKIEVPHDFFMTWAQLREMAQSGLVELASHSHNLHRGVLANPQGNEQPAASSRQYLPASGRYENDAEYRARVRQDLKTSAHLIRHHTGVTIRSIVWPYGAHNRDTDQVAAEVGLNIGLTLQPGPNTPDVALTQIRRSLVDYEVN
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
view details
3.1 7-261 255 1-6, 262-264 6 3 knot
view details
2.1 7-258 252 1-6 262-264 259-261 6 3 slipknot
publication title The Protein BpsB Is a Poly-beta-1,6-N-acetyl-d-glucosamine Deacetylase Required for Biofilm Formation in Bordetella bronchiseptica.
pubmed doi rcsb
structure length 264
molecule tags Hydrolase
source organism Bordetella bronchiseptica rb50
sequence length 264
molecule keywords BpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
ec nomenclature ec 3.5.1.33: N-acetylglucosamine deacetylase.
pdb deposition date 2015-06-03
KnotProt deposition date 2018-10-20
Image from the rcsb pdb (www.rcsb.org)
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
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