5L8MA

Wild-type pas-gaf fragment from deinococcus radiodurans bphp collected at lcls
Warning
  • Chain breaks within knot 41 (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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 41 41
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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41 28-268 241 1-27, 269-316 27 48 knot
Chain Sequence
PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPA--HLSLTVHRVGELLILEFEPTELR---------NAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAL
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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3.2m 27-253 227 1-26 263-305 254-262 26 43 slipknot
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4.1 7-262 256 1-6 266-305 263-265 6 40 slipknot
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4.1 25-264 240 1-24 276-305 265-275 24 30 slipknot
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3.2m 27-276 250 1-26 294-305 277-293 26 12 slipknot
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3.2m 11-262 252 1-6, 265-305 7-10, 263-264 6 41 slipknot
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4.1 26-296 271 297-305 1-7 8-25 7 8 slipknot
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3.2 31-296 266 297-305 1-25 26-30 25 8 slipknot
missing residues 102-103, 125-133
publication title The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography.
pubmed doi rcsb
structure length 305
molecule tags Transferase
source organism Deinococcus radiodurans
sequence length 316
molecule keywords Bacteriophytochrome
ec nomenclature
pdb deposition date 2016-06-08
KnotProt deposition date 2016-11-08
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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