4O01B

Crystal structure of d. radiodurans bacteriophytochrome photosensory core module in its illuminated 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

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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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41 30-270 241 1-29, 271-501 29 231 knot
Chain Sequence
LPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDW--AGHLSLTVHRVGELLILEFEPTEWD-SGPH-ALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVADLGP-----------RHSFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGALEHHH
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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4.1 29-304 276 1-28, 305-486 28 182 knot
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3.2m 26-261 236 1-25 272-486 262-271 25 215 slipknot
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4.1 7-271 265 1-6 276-486 272-275 6 211 slipknot
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3.2m 27-284 258 1-26 304-486 285-303 26 183 slipknot
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4.1 31-306 276 1-28, 450-486 29-30, 307-449 28 37 slipknot
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4.1 32-310 279 1-30, 447-486 31-31, 311-446 30 40 slipknot
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3.2m 31-266 236 1-25, 276-486 26-30, 267-275 25 211 slipknot
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3.2 32-449 418 1-28, 474-486 29-31, 450-473 28 13 slipknot
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4.1 32-473 442 474-486 1-28 29-31 28 12 slipknot
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3.2 33-324 292 1-31, 446-486 32-32, 325-445 31 41 slipknot
sequence length 501
structure length 486
publication title Signal amplification and transduction in phytochrome photosensors
pubmed doi rcsb
molecule tags Transferase
molecule keywords Bacteriophytochrome
source organism Deinococcus radiodurans r1
missing residues 101-102, 126, 130, 446-456
ec nomenclature ec 2.7.13.3: Histidine kinase.
pdb deposition date 2013-12-13
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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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling