PDB
3AYM
Resolution
2.8 Å
Released
Aug. 17, 2011
Receptor
Rhodopsin
Class
A
Species
Todarodes pacificus
Ligand
all-trans-retinal
Function
Agonist
Reference
10.1016/J.JMB.2011.08.044

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Ligand Amino Acid Generic Number Segment Interaction Type
all-trans-retinal F120 3.37x37 TM3 hydrophobic
all-trans-retinal I123 3.40x40 TM3 hydrophobic
all-trans-retinal F188 45.52x52 ECL2 hydrophobic
all-trans-retinal F205 5.43x44 TM5 hydrophobic
all-trans-retinal F209 5.47x47 TM5 hydrophobic
all-trans-retinal F270 6.44x44 TM6 hydrophobic
all-trans-retinal W274 6.48x48 TM6 hydrophobic
all-trans-retinal A278 6.52x52 TM6 hydrophobic
all-trans-retinal V301 7.39x38 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
Rhodopsin
TM3
3x37 3.37x37 F120
3x40 3.40x40 I123
ECL2
45x52 45.52x52 F188
TM5
5x44 5.43x44 F205
5x47 5.47x47 F209
TM6
6x44 6.44x44 F270
6x48 6.48x48 W274
6x52 6.52x52 A278
TM7
7x38 7.39x38 V301