4QRVA

Crystal structure of i86f mutant of papain
Warning
  • Chain breaks within knot 31 (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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 109
Knot K -31 -31 -31

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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
view details
-31 93-226 134 1-92, 227-316 92 90 knot
Chain Sequence
IVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGS----YTTTEVNIP-----------EYVDWRQKGAVTPVKNQGSCGSAWAFSAVSTIESIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIRNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN
Note, that the numbers in the matrix denote the consecutive residues in the loop, not the index of amino acids in the chain!
Knot K 6x -31 -31 1x -31 -31 -31 -31 -31

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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
- 31 95-226 132 1-94, 227-270 94 44 knot
Fingerprint Knot forming loop Loop type
K -31 Ile4 ... Cys260 <-> Cys307 ...
Chain closureAsn319 <-> Ile4
 probabilistic
K -31 Ile4 ... Cys163 <-> Cys202 ...
Chain closureAsn319 <-> Ile4
 probabilistic
K -31 Ile4 ... Cys129 <-> Cys170 ...
Chain closureAsn319 <-> Ile4
 probabilistic
K -31 Ile4 ... Cys163 <-> Cys202 ... Cys260 <-> Cys307 ...
Chain closureAsn319 <-> Ile4
 probabilistic
K -31 Ile4 ... Cys129 <-> Cys170 ... Cys260 <-> Cys307 ...
Chain closureAsn319 <-> Ile4
 probabilistic
K -31 Ile4 ... Cys129 <-> Cys170 ... Cys163 <-> Cys202 ...
Chain closureAsn319 <-> Ile4
 probabilistic
K -31 Ile4 ... Cys129 <-> Cys170 ... Cys163 <-> Cys202 ... Cys260 <-> Cys307 ...
Chain closureAsn319 <-> Ile4
 probabilistic
Chain Sequence
IVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGS----YTTTEVNIP-----------EYVDWRQKGAVTPVKNQGSCGSAWAFSAVSTIESIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIRNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN
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
view details
2.1m 92-224 133 1-91 237-316 225-236 91 80 slipknot
view details
2.1m 65-263 199 1-64 270-316 264-269 64 47 slipknot
view details
2.1m 91-312 222 313-316 1-86 87-90 86 3 slipknot
sequence length 316
structure length 301
publication title Pro-peptide regulates the substrate specificity and zymogen activation process of papain: A structural and mechanistic insight
rcsb
molecule tags Hydrolase
molecule keywords Papain
source organism Carica papaya
missing residues 83-86, 92-102
total genus Genus: 109
ec nomenclature ec 3.4.22.2: Papain.
pdb deposition date 2014-07-02
KnotProt deposition date 2018-10-19

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00112 Peptidase_C1 Papain family cysteine protease
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