5MG0A

Structure of pas-gaf fragment of deinococcus phytochrome by serial femtosecond crystallography
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 30-271 242 1-29, 272-324 29 53 knot
Chain Sequence
DPLPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWP--GHLSLTVHRVGELLILEFEPTEAWDSTGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLESLGRLLSLQVQVKEAHHHHHH
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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4.1 29-313 285 1-28, 314-324 28 11 knot
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3.2m 29-267 239 1-28 277-324 268-276 28 48 slipknot
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3.2m 30-277 248 1-29 289-324 278-288 29 36 slipknot
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3.2m 20-288 269 1-2, 290-324 3-19, 289-289 2 35 slipknot
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3.2m 29-290 262 1-28 314-324 291-313 28 11 slipknot
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3.2 34-309 276 310-324 1-28 29-33 28 14 slipknot
missing residues 104-105
publication title Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.
pubmed doi rcsb
structure length 322
molecule tags Transferase
source organism Deinococcus radiodurans (strain atcc 13939 / dsm 20539 / jcm 16871 / lmg 4051 /
sequence length 324
total genus Genus: 96
molecule keywords Bacteriophytochrome
ec nomenclature
pdb deposition date 2016-11-20
KnotProt deposition date 2018-09-12
Image from the rcsb pdb (www.rcsb.org)
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similar chains in the pdb database (?% sequence similarity)

 
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