5ZNMA

Colicin d central domain and c-terminal trnase domain
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 90
Slipknot S +31 +31 +31 +31

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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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+31 166-263 98 1-165 279-387 264-278 165 109 slipknot
Chain Sequence
MHEEAVARAEAEKAKAELFSKAGVNQPPVYTQEMMERANSVMNEQGALVLNNTASSVQLAMTGTGVWTAAGDIAGNISKFFSNALEKVT----SPLLMRISLGANLEA------------------MFSLSAQMLAGQGVVIEPGATSVNLPVRGQLINSNGQLALDLLKTGNESIPAAVPVLNAVRDTATGLDKITLPAVVGAPSRTILVNPVPQPSVPTDTGNHQPVPVTPVHTGTEVKSVEMPVDVGGLRDFIYWRPDAAGTGVEA-------VYVMLNDPLDSGRFSRKQLDKKYKHAGDFGISDTKKNRETLTKFRDAIEEHLSDKDTVEKGTYRREKGSKVYFNPNTMNVVIIKSNGEFLSGWKINPDADNGRIYLETGEL
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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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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3.1 49-263 215 1-48 277-387 264-276 48 111 slipknot
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2.1 66-263 198 1-58, 278-387 59-65, 264-277 58 110 slipknot
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2.1 128-264 137 1-102, 277-387 103-127, 265-276 102 111 slipknot
sequence length 387
structure length 358
publication title Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell
pubmed doi rcsb
molecule tags Antibiotic
molecule keywords Colicin-D
source organism Escherichia coli
missing residues 90-93, 105-122, 248-254
total genus Genus: 90
ec nomenclature
pdb deposition date 2018-04-10
KnotProt deposition date 2018-09-13
Image from the rcsb pdb (www.rcsb.org)
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similar chains in the pdb database (?% sequence similarity)

  
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling