4I6NA

Crystal structure of trichinella spiralis uch37 catalytic domain bound to ubiquitin vinyl methyl ester
Warning
  • Chain breaks within knot 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
  • Chain breaks within knot 52 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Knot K -52 -31 -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 12-166 155 1-11 224-229 167-223 11 6 slipknot
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-52 12-225 214 1-11, 226-229 11 4 knot
Chain Sequence
PLGSMAEGNWCLIESDPGIFTEMIHGFGCTGLQVEELVVLDESIEHLKPIHGFIFLFRWLKKEMRKEVDDSPQTCTDVYFSQQVIQNACASQALINLLLNCDHPDVDLGPTLKEFKDFTYDLDSASRGLCLTNSEKIRAVHNSFG----------QKLDEEDVFHFVTYVPVNDGVYELDGLRAAPLRLGTVASDGDWTEVAIKAIKEKIKNYGESEVRFNLMAVISDQ
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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5.2m 10-215 206 1-9, 216-219 9 4 knot
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2.1m 11-155 145 1-10 161-219 156-160 10 59 slipknot
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3.1m 10-160 151 1-9 168-219 161-167 9 52 slipknot
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3.1m 11-164 154 1-10 172-219 165-171 10 48 slipknot
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2.1m 11-172 162 1-10 179-219 173-178 10 41 slipknot
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3.1m 11-178 168 1-10 214-219 179-213 10 6 slipknot
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3.1m 12-178 167 1-10, 213-219 11-11, 179-212 10 7 slipknot
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2.1m 14-196 183 1-11, 206-219 12-13, 197-205 11 14 slipknot
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2.1m 14-205 192 1-11, 211-219 12-13, 206-210 11 9 slipknot
missing residues 146-155
publication title Stabilization of an Unusual Salt Bridge in Ubiquitin by the Extra C-Terminal Domain of the Proteasome-Associated Deubiquitinase UCH37 as a Mechanism of Its Exo Specificity.
pubmed doi rcsb
structure length 219
molecule tags Hydrolase/signaling protein
source organism Trichinella spiralis
sequence length 229
total genus Genus: 64
molecule keywords Ubiquitin carboxyl-hydrolase
ec nomenclature
pdb deposition date 2012-11-29
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01088 Peptidase_C12 Ubiquitin carboxyl-terminal hydrolase, family 1
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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