PDB
9VMG
Resolution
2.8 Å
Released
May 13, 2026
Receptor
A0A678XLR1
Class
A
Species
Petromyzon marinus
Ligand
spermine
Function
Agonist
Reference
10.1038/S41421-025-00839-4

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Ligand Amino Acid Generic Number Segment Interaction Type
spermine D112 3.32x32 TM3 polar (charge-assisted hydrogen bond)
spermine Y113 3.33x33 TM3 hydrophobic
spermine Y113 3.33x33 TM3 Van der Waals
spermine C116 3.36x36 TM3 Van der Waals
spermine C116 3.36x36 TM3 hydrophobic
spermine V190 45.52x52 ECL2 Van der Waals
spermine V190 45.52x52 ECL2 polar (hydrogen bond with backbone)
spermine W267 6.48x48 TM6 Van der Waals
spermine Y270 6.51x51 TM6 polar (hydrogen bond)
spermine Y270 6.51x51 TM6 Van der Waals
spermine E277 6.58x58 TM6 polar (charge-assisted hydrogen bond)
spermine W289 7.35x34 TM7 hydrophobic
spermine W289 7.35x34 TM7 Van der Waals
spermine N293 7.39x38 TM7 polar (hydrogen bond)
spermine N293 7.39x38 TM7 Van der Waals

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Snake plot — Download: PNG | SVG
ICL1 R Q L Q T R ICL1ECL1 C W F Y ECL1ICL2 P L R Y E Q R V ICL2ECL2 E W N L V G L E E E V A H I C P D D C P V L L ECL2ICL3 V ICL3ECL3 Y H A ECL3N-term M S S H A N T T S P A C G L T F Y D F N C S R A S V T N-termC-term G R M F A S S C R G V D L F D V L R A L A K A R G C-term S S S E R A Q V M S L L L S I S A I T I A G N L L T I T S I L Y F T N V L T L S L A V A D L L V G L L I M P F S V M R S V H N G R V F C R V H T W L D Y T F C T S S I V H L S C I S F D R Y V A I S D T R R A C V R M L V C C W L C L L V Y G L A F M M N L P F A M A N T I F A C I V P M M L M T L A Y G R I Y Q L A R Q Q A R K I T S A A G S N A D S A R S S L R R E H S A T I T M G I I V G V F I S L W I P Y F V V S V T E P I F G S S V T W E V I N W F T Y I N S T A N P I L F A A F N R P F Y L I R N A F L S
Helix box plot — Download: PNG | SVG L N G A I T I A S I S L L L S M V Q A R 1 L S L A V A D L L V G L L I M P F S V M R 2 C S L H V I S S T C F T Y D L W T H V R 3 C V R M L V C C W L C L L V Y G L A F M 4 A L T M L M M P V I C A F I T N A M A F P 5 G I I V G V F I S L W I P Y F V V S V T 6 I P N A T S N I Y T F W N I V E W T V 7

GPCRdb(A)
GPCRdb(A)
A0A678XLR1
TM3
3x32 3.32x32 D112
3x33 3.33x33 Y113
3x36 3.36x36 C116
ECL2
45x52 45.52x52 V190
TM6
6x48 6.48x48 W267
6x51 6.51x51 Y270
6x58 6.58x58 E277
TM7
7x34 7.35x34 W289
7x38 7.39x38 N293