5JDFA

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 1mm ca2+
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Knot K +31
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 41-229 189 1-40, 230-301 40 72 knot
Chain Sequence
MVILGVGYFLLGLILLYYGSDWFVLGSERIARHFNVSNFVIGATVMAIGTSLPEILTSAYASYMHAPGISIGNAIGSCICNIGLVLGLSAIISPIIVDKNLQKNILVYLLFVIFAAVIGIDGFSWIDGVVLLILFIIYLRWTVKNGSA-------KNNPSVVFSLVLLIIGLIGVLVGAELFVDGAKKIALALDISDKVIGFTLVAFGTSLPELMVSLAAAKRNLGGMVLGNVIGSNIADIGGALAVGSLFMHLPAENVQMAVLVIMSLLLYLFAKYSKIGRWQGILFLALYIIAIASLRM
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 29x +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 41-225 185 1-40, 226-297 40 72 knot
Fingerprint Knot forming loop Loop type
K +31 Met1 ... Asp121 <->
Bridging ionCa401
<-> Asp127 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Thr209 <->
Bridging ionCa402
<-> Glu213 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Thr209 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionCa402
<-> Glu54 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Glu213 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Gly122 <->
Bridging ionCa401
<-> Asp127 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Asp127 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Asp121 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Gly122 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Asp121 <->
Bridging ionCa401
<-> Asp127 ... Thr209 <->
Bridging ionCa402
<-> Glu213 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Asp121 <->
Bridging ionCa401
<-> Asp127 ... Thr209 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionCa402
<-> Glu54 ... Asp121 <->
Bridging ionCa401
<-> Asp127 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Asp121 <->
Bridging ionCa401
<-> Asp127 ... Glu213 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Gly122 <->
Bridging ionCa401
<-> Asp127 ... Thr209 <->
Bridging ionCa402
<-> Glu213 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Gly122 <->
Bridging ionCa401
<-> Asp127 ... Thr209 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionCa402
<-> Glu54 ... Gly122 <->
Bridging ionCa401
<-> Asp127 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Gly122 <->
Bridging ionCa401
<-> Asp127 ... Glu213 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Asp127 ... Thr209 <->
Bridging ionCa402
<-> Glu213 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Asp127 ... Thr209 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionCa402
<-> Glu54 ... Ile118 <->
Bridging ionCa401
<-> Asp127 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Asp127 ... Glu213 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Asp121 ... Thr209 <->
Bridging ionCa402
<-> Glu213 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Asp121 ... Thr209 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionCa402
<-> Glu54 ... Ile118 <->
Bridging ionCa401
<-> Asp121 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Asp121 ... Glu213 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Gly122 ... Thr209 <->
Bridging ionCa402
<-> Glu213 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Gly122 ... Thr209 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Thr50 <->
Bridging ionCa402
<-> Glu54 ... Ile118 <->
Bridging ionCa401
<-> Gly122 ...
Chain closureMet301 <-> Met1
probabilistic
K +31 Met1 ... Ile118 <->
Bridging ionCa401
<-> Gly122 ... Glu213 <->
Bridging ionCa402
<-> Asp240 ...
Chain closureMet301 <-> Met1
probabilistic
Chain Sequence
MVILGVGYFLLGLILLYYGSDWFVLGSERIARHFNVSNFVIGATVMAIGTSLPEILTSAYASYMHAPGISIGNAIGSCICNIGLVLGLSAIISPIIVDKNLQKNILVYLLFVIFAAVIGIDGFSWIDGVVLLILFIIYLRWTVKNGSA-------KNNPSVVFSLVLLIIGLIGVLVGAELFVDGAKKIALALDISDKVIGFTLVAFGTSLPELMVSLAAAKRNLGGMVLGNVIGSNIADIGGALAVGSLFMHLPAENVQMAVLVIMSLLLYLFAKYSKIGRWQGILFLALYIIAIASLRM
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
view details
3.1 20-248 229 1-19, 249-301 19 53 knot
view details
3.1 23-243 221 1-6, 256-301 7-22, 244-255 6 46 slipknot
view details
2.1 43-237 195 238-301 1-8 9-42 8 63 slipknot
view details
2.1 52-246 195 247-301 1-42 43-51 42 54 slipknot
missing residues 149-155
publication title Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger.
pubmed doi rcsb
structure length 294
molecule tags Membrane protein
source organism Methanocaldococcus jannaschii
sequence length 301
total genus Genus: 121
molecule keywords Uncharacterized membrane protein MJ0091
ec nomenclature
pdb deposition date 2016-04-16
KnotProt deposition date 2018-10-20
Image from the rcsb pdb (www.rcsb.org)
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