4DJKA

Structure of glutamate-gaba antiporter gadc
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 140
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 30-212 183 1-17, 455-490 18-29, 213-454 17 36 slipknot
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41 16-244 229 1-15 289-490 245-288 15 202 slipknot
Chain Sequence
QLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGW---GVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHTFF------------PDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHFFLHPRARSP
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 7-223 217 1-6 230-451 224-229 6 222 slipknot
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3.2 6-231 226 1-5 238-451 232-237 5 214 slipknot
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3.2m 9-251 243 1-8 261-451 252-260 8 191 slipknot
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3.2 19-256 238 1-7, 270-451 8-18, 257-269 7 182 slipknot
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3.2 19-269 251 1-7, 275-451 8-18, 270-274 7 177 slipknot
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3.2 21-256 236 1-18, 270-451 19-20, 257-269 18 182 slipknot
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2.3 16-225 210 1-11, 232-451 12-15, 226-231 11 220 slipknot
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2.1 35-193 159 1-13, 214-451 14-34, 194-213 13 238 slipknot
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2.1 34-296 263 1-13, 345-451 14-33, 297-344 13 107 slipknot
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2.1 31-185 155 1-15, 194-451 16-30, 186-193 15 258 slipknot
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1.1 33-217 185 1-15, 231-451 16-32, 218-230 15 221 slipknot
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2.3 21-230 210 1-16, 233-451 17-20, 231-232 16 219 slipknot
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2.3 22-230 209 1-20, 233-451 21-21, 231-232 20 219 slipknot
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1.1 32-185 154 1-30, 194-451 31-31, 186-193 30 258 slipknot
sequence length 490
structure length 451
publication title Structure and mechanism of a glutamate-GABA antiporter
pubmed doi rcsb
molecule tags Transport protein
molecule keywords Probable glutamate/gamma-aminobutyrate antiporter
source organism Escherichia coli
missing residues 60-62, 170-181, 456-479
total genus Genus: 140
ec nomenclature
pdb deposition date 2012-02-02
KnotProt deposition date 2014-09-29

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF13520 AA_permease_2 Amino acid permease
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