3DH4A

Crystal structure of sodium/sugar symporter with bound galactose from vibrio parahaemolyticus
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
  • 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 169
Slipknot S +31 41 +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
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+31 54-244 191 245-518 1-36 37-53 36 273 slipknot
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41 31-275 245 1-30 335-518 276-334 30 184 slipknot
Chain Sequence
XXXXXXXXXXXXXXXXXAGKSLPWWAVGASLIAANISAEQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLKTILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSILGLALFALVYSI------VVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSNPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFLVVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWLTQFLPVGVKGVVFAALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLGGIGQAFQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPLSMPFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVTSSMFVTDRSFNIAAYGIMIVLAVLYTLFWVLYK
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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3.2 27-264 238 1-26 278-512 265-277 26 235 slipknot
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4.1 28-274 247 1-27 301-512 275-300 27 212 slipknot
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4.1 28-300 273 1-27 304-512 301-303 27 209 slipknot
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4.1 26-304 279 1-25 322-512 305-321 25 191 slipknot
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4.1 28-316 289 1-5, 324-512 6-27, 317-323 5 189 slipknot
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4.1 28-323 296 1-5, 330-512 6-27, 324-329 5 183 slipknot
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3.2 30-298 269 1-11, 305-512 12-29, 299-304 11 208 slipknot
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3.2 30-304 275 1-25, 307-512 26-29, 305-306 25 206 slipknot
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3.2 30-306 277 1-25, 312-512 26-29, 307-311 25 201 slipknot
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3.2 31-306 276 1-25, 321-512 26-30, 307-320 25 192 slipknot
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3.2 31-320 290 1-27, 327-512 28-30, 321-326 27 186 slipknot
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3.2 31-326 296 1-27, 330-512 28-30, 327-329 27 183 slipknot
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3.2 34-306 273 1-30, 321-512 31-33, 307-320 30 192 slipknot
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3.2 34-320 287 1-30, 327-512 31-33, 321-326 30 186 slipknot
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3.2m 35-299 265 1-29, 306-512 30-34, 300-305 29 207 slipknot
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3.2m 35-305 271 1-29, 307-512 30-34, 306-306 29 206 slipknot
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3.2m 35-306 272 1-33, 317-512 34-34, 307-316 33 196 slipknot
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3.2 36-301 266 1-34, 317-512 35-35, 302-316 34 196 slipknot
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3.2 35-281 247 1-27, 293-512 28-34, 282-292 27 220 slipknot
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2.1 63-331 269 1-32, 380-512 33-62, 332-379 32 133 slipknot
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2.1 60-396 337 397-512 1-33 34-59 33 115 slipknot
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2.1 59-231 173 1-35, 245-512 36-58, 232-244 35 268 slipknot
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2.1 47-254 208 1-37, 261-512 38-46, 255-260 37 252 slipknot
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2.1 51-259 209 1-43, 272-512 44-50, 260-271 43 241 slipknot
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1.1 64-256 193 1-46, 274-512 47-63, 257-273 46 239 slipknot
sequence length 518
structure length 512
publication title The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport.
pubmed doi rcsb
molecule tags Transport protein
molecule keywords Sodium/glucose cotransporter
source organism Vibrio parahaemolyticus
missing residues 150-155
total genus Genus: 169
ec nomenclature
pdb deposition date 2008-06-16
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00474 SSF Sodium:solute symporter family
Image from the rcsb pdb (www.rcsb.org)
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling