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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
total genus Genus: 89
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 pdb database (?% sequence similarity)

 
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