5JDMA

Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger ncx_mj soaked with 2.5 mm na+ and 0.1mm sr2+
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 126
Knot K +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 41-233 193 1-40, 234-300 40 67 knot
Chain Sequence
MVILGVGYFLLGLILLYYGSDWFVLGSERIARHFNVSNFVIGATVMAIGTSLPEILTSAYASYMHAPGISIGNAIGSCICNIGLVLGLSAIISPIIVDKNLQKNILVYLLFVIFAAVIGIDGFSWIDGVVLLILFIIYLRWTVKNGSAEIE------NPSVVFSLVLLIIGLIGVLVGAELFVDGAKKIALALDISDKVIGFTLVAFGTSLPELMVSLAAAKRNLGGMVLGNVIGSNIADIGGALAVGSLFMHLPAENVQMAVLVIMSLLLYLFAKYSKIGRWQGILFLALYIIAIASLR
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 39x +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 39-226 188 1-38, 227-293 38 67 knot
Fingerprint Knot forming loop Loop type
K +31 Met1 ... Ile118 <->
Bridging ionSr403
<-> Asp127 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Ala47 <->
Bridging ionNa401
<-> Ser51 ... Ile118 <->
Bridging ionSr403
<-> Asp127 ... Glu213 <->
Bridging ionNa401
<-> Thr50 ... Ala47		 ion-based
K +31 Glu54 ... Ile118 <->
Bridging ionSr403
<-> Asp127 ... Glu213 <->
Bridging ionNa402
<-> Glu54		 ion-based
K +31 Ala47 <->
Bridging ionNa401
<-> Ser51 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ... Glu213 <->
Bridging ionNa401
<-> Thr50 ... Ala47		 ion-based
K +31 Thr50 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ... Glu213 <->
Bridging ionNa401
<-> Thr50		 ion-based
K +31 Thr50 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ... Ser236 <->
Bridging ionNa401
<-> Thr50		 ion-based
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ... Ile118 <->
Bridging ionSr403
<-> Asp127 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionSr403
<-> Asp127 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionNa401
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ... Thr50 <->
Bridging ionNa401
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Glu54 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Thr50 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ... Thr209 <->
Bridging ionNa402
<-> Thr50		 ion-based
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionNa402
<-> Glu54 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Ala47 <->
Bridging ionNa401
<-> Ser51 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ... Glu213 <->
Bridging ionNa401
<-> Thr50 ... Ala47		 ion-based
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ... Thr50 <->
Bridging ionNa402
<-> Glu54 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Ala47 <->
Bridging ionNa401
<-> Thr50 ... Ala47		 ion-based
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Thr50 ... Ile118 <->
Bridging ionSr403
<-> Asp127 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Thr50 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ... Ser236 <->
Bridging ionNa401
<-> Thr50		 ion-based
K +31 Thr50 <->
Bridging ionNa402
<-> Glu54 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ... Ser236 <->
Bridging ionNa401
<-> Thr50		 ion-based
K +31 Thr50 <->
Bridging ionNa401
<-> Glu213 ... Thr209 <->
Bridging ionNa402
<-> Glu54 ... Thr50		 ion-based
K +31 Thr50 <->
Bridging ionNa402
<-> Glu54 ... Ile118 <->
Bridging ionSr403
<-> Asp127 ... Glu213 <->
Bridging ionNa401
<-> Thr50		 ion-based
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ... Ile118 <->
Bridging ionSr403
<-> Asp127 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionNa402
<-> Glu54 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Ala47 <->
Bridging ionNa401
<-> Ser51 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ... Thr209 <->
Bridging ionNa402
<-> Thr50 ... Ala47		 ion-based
K +31 Glu54 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ... Thr209 <->
Bridging ionNa402
<-> Glu54		 ion-based
K +31 Thr50 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ... Thr209 <->
Bridging ionNa402
<-> Thr50		 ion-based
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Ser51 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Glu54 ... Ile118 <->
Bridging ionSr403
<-> Asp121 ... Glu213 <->
Bridging ionNa402
<-> Glu54		 ion-based
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Thr50 ... Thr209 <->
Bridging ionNa402
<-> Glu213 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Met1 ... Ala47 <->
Bridging ionNa401
<-> Thr50 ... Glu54 <->
Bridging ionNa402
<-> Thr209 ...
Chain closureArg300 <-> Met1
 probabilistic
K +31 Thr50 <->
Bridging ionNa401
<-> Glu213 ... Thr209 <->
Bridging ionNa402
<-> Thr50		 ion-based
K +31 Thr50 <->
Bridging ionNa402
<-> Glu54 ... Glu213 <->
Bridging ionNa401
<-> Thr50		 ion-based
K +31 Thr50 <->
Bridging ionNa402
<-> Glu54 ... Asp121 <->
Bridging ionSr403
<-> Asp127 ... Glu213 <->
Bridging ionNa401
<-> Thr50		 ion-based
Chain Sequence
MVILGVGYFLLGLILLYYGSDWFVLGSERIARHFNVSNFVIGATVMAIGTSLPEILTSAYASYMHAPGISIGNAIGSCICNIGLVLGLSAIISPIIVDKNLQKNILVYLLFVIFAAVIGIDGFSWIDGVVLLILFIIYLRWTVKNGSAEIE------NPSVVFSLVLLIIGLIGVLVGAELFVDGAKKIALALDISDKVIGFTLVAFGTSLPELMVSLAAAKRNLGGMVLGNVIGSNIADIGGALAVGSLFMHLPAENVQMAVLVIMSLLLYLFAKYSKIGRWQGILFLALYIIAIASLR
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


  Help Knotoid subchains data interpretation Full screen
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
3.1 20-247 228 1-19, 248-300 19 53 knot
view details
3.1 23-236 214 1-5, 258-300 6-22, 237-257 5 43 slipknot
view details
2.1 44-236 193 237-300 1-19 20-43 19 63 slipknot
view details
2.1 51-251 201 252-300 1-43 44-50 43 48 slipknot
view details
2.1 52-261 210 1-50, 297-300 51-51, 262-296 50 4 slipknot
sequence length 300
structure length 294
publication title Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger.
pubmed doi rcsb
molecule tags Membrane protein
molecule keywords sodium-calcium exchanger NCX_Mj
source organism Methanocaldococcus jannaschii (strain atcc 43067 / dsm 2661 / jal-1 / jcm 10045 / nbrc 100440)
missing residues 152-157
total genus Genus: 126
ec nomenclature
pdb deposition date 2016-04-17
KnotProt deposition date 2018-10-17
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)

  
#similar chains in the KnotProt database (?% sequence similarity)
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#similar chains, but unknotted
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling