PDB
9YDA
Resolution
2.9 Å
Released
Dec. 24, 2025
Receptor
OPN1MW
Class
A
Species
Homo sapiens
Ligand
Function
all-trans-retinal
Agonist
Reference
10.1073/PNAS.2516318122

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Ligand Amino Acid Generic Number Segment Interaction Type
all-trans-retinal E102 2.53x53 TM2 Van der Waals
all-trans-retinal G137 3.36x36 TM3 Van der Waals
all-trans-retinal I138 3.37x37 TM3 Van der Waals
all-trans-retinal L223 5.42x43 TM5 hydrophobic
all-trans-retinal M224 5.43x44 TM5 hydrophobic
all-trans-retinal C227 5.46x461 TM5 Van der Waals
all-trans-retinal C228 5.47x47 TM5 hydrophobic
all-trans-retinal W281 6.48x48 TM6 hydrophobic
all-trans-retinal Y284 6.51x51 TM6 Van der Waals
all-trans-retinal A288 6.55x55 TM6 hydrophobic
all-trans-retinal K312 7.43x42 TM7 covalent bond

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

GPCRdb(A)
GPCRdb(A)
OPN1MW
TM2
2x53 2.53x53 E102
TM3
3x36 3.36x36 G137
3x37 3.37x37 I138
TM5
5x43 5.42x43 L223
5x44 5.43x44 M224
5x461 5.46x461 C227
5x47 5.47x47 C228
TM6
6x48 6.48x48 W281
6x51 6.51x51 Y284
6x55 6.55x55 A288
TM7
7x42 7.43x42 K312