PDB
3C9M
Resolution
3.4 Å
Released
Aug. 5, 2008
Receptor
Rhodopsin
Class
A
Species
Bos taurus
Ligand
Function
all-trans-retinal
Inverse agonist
Reference
10.1107/S0907444908017162

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Ligand Amino Acid Generic Number Segment Interaction Type
all-trans-retinal E113 3.28x28 TM3 Van der Waals
all-trans-retinal G114 3.29x29 TM3 Van der Waals
all-trans-retinal A117 3.32x32 TM3 hydrophobic
all-trans-retinal T118 3.33x33 TM3 Van der Waals
all-trans-retinal G121 3.36x36 TM3 Van der Waals
all-trans-retinal E122 3.37x37 TM3 Van der Waals
all-trans-retinal E181 ECL2 Van der Waals
all-trans-retinal S186 ECL2 Van der Waals
all-trans-retinal C187 45.50x50 ECL2 Van der Waals
all-trans-retinal G188 45.51x51 ECL2 Van der Waals
all-trans-retinal I189 45.52x52 ECL2 hydrophobic
all-trans-retinal Y191 ECL2 Van der Waals
all-trans-retinal M207 5.42x43 TM5 hydrophobic
all-trans-retinal H211 5.46x461 TM5 Van der Waals
all-trans-retinal F212 5.47x47 TM5 hydrophobic
all-trans-retinal F261 6.44x44 TM6 hydrophobic
all-trans-retinal W265 6.48x48 TM6 hydrophobic
all-trans-retinal Y268 6.51x51 TM6 hydrophobic
all-trans-retinal A269 6.52x52 TM6 hydrophobic
all-trans-retinal A292 7.39x38 TM7 Van der Waals
all-trans-retinal K296 7.43x42 TM7 covalent bond

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

GPCRdb(A)
GPCRdb(A)
Rhodopsin
TM3
3x28 3.28x28 E113
3x29 3.29x29 G114
3x32 3.32x32 A117
3x33 3.33x33 T118
3x36 3.36x36 G121
3x37 3.37x37 E122
ECL2
45x50 45.50x50 C187
45x51 45.51x51 G188
45x52 45.52x52 I189
TM5
5x43 5.42x43 M207
5x461 5.46x461 H211
5x47 5.47x47 F212
TM6
6x44 6.44x44 F261
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x52 6.52x52 A269
TM7
7x38 7.39x38 A292
7x42 7.43x42 K296