PDB
8Y02
Resolution
2.6 Å
Released
June 11, 2025
Receptor
OPN1SW
Class
A
Species
Homo sapiens
Ligand
Function
all-trans-retinal
Agonist
Reference
10.1126/SCIENCE.ADZ8141

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Ligand Amino Acid Generic Number Segment Interaction Type
all-trans-retinal L83 2.53x53 TM2 hydrophobic
all-trans-retinal S87 2.57x56 TM2 Van der Waals
all-trans-retinal G114 3.32x32 TM3 Van der Waals
all-trans-retinal L119 3.37x37 TM3 hydrophobic
all-trans-retinal W188 ECL2 Van der Waals
all-trans-retinal L204 5.42x43 TM5 hydrophobic
all-trans-retinal F205 5.43x44 TM5 hydrophobic
all-trans-retinal C208 5.46x461 TM5 hydrophobic
all-trans-retinal F209 5.47x47 TM5 hydrophobic
all-trans-retinal Y262 6.48x48 TM6 hydrophobic
all-trans-retinal Y265 6.51x51 TM6 hydrophobic
all-trans-retinal A266 6.52x52 TM6 hydrophobic
all-trans-retinal A269 6.55x55 TM6 hydrophobic
all-trans-retinal S289 7.39x38 TM7 Van der Waals
all-trans-retinal K293 7.43x42 TM7 covalent bond

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

GPCRdb(A)
GPCRdb(A)
OPN1SW
TM2
2x53 2.53x53 L80
2x56 2.57x56 S84
TM3
3x32 3.32x32 G111
3x37 3.37x37 L116
TM5
5x43 5.42x43 L201
5x44 5.43x44 F202
5x461 5.46x461 C205
5x47 5.47x47 F206
TM6
6x48 6.48x48 Y259
6x51 6.51x51 Y262
6x52 6.52x52 A263
6x55 6.55x55 A266
TM7
7x38 7.39x38 S286
7x42 7.43x42 K290