4O0PB

Crystal structure of d. radiodurans bacteriophytochrome photosensory core module in its dark form
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 32-271 240 1-31, 272-500 31 229 knot
Chain Sequence
DPLPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWP---HLSLTVHRVGELLILEFEPTEHAL-------RNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGLVQTDALGQL-WPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVAWGGATPDLGPRHSFDTYL-----EEKRGYAEPWHPGEIEEAQDLRDTLTGALE
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 30-302 273 1-29, 303-484 29 182 knot
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3.2m 30-257 228 1-29 266-484 258-265 29 219 slipknot
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4.1 12-265 254 1-11 272-484 266-271 11 213 slipknot
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4.1 30-267 238 1-29 278-484 268-277 29 207 slipknot
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3.2m 29-277 249 1-28 279-484 278-278 28 206 slipknot
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3.2m 30-280 251 1-29 303-484 281-302 29 182 slipknot
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4.1 33-297 265 1-29, 338-484 30-32, 298-337 29 147 slipknot
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3.2 34-304 271 305-484 1-29 30-33 29 179 slipknot
missing residues 104-106, 128-134, 398, 455-459
publication title Signal amplification and transduction in phytochrome photosensors
pubmed doi rcsb
structure length 484
molecule tags Transferase
source organism Deinococcus radiodurans
sequence length 500
molecule keywords Bacteriophytochrome
ec nomenclature ec 2.7.13.3: Histidine kinase.
pdb deposition date 2013-12-14
KnotProt deposition date 2014-08-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF00360 PHY Phytochrome region
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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