PDB
6PGS
Resolution
2.9 Å
Released
July 1, 2020
Receptor
Rhodopsin
Class
A
Species
Bos taurus
Ligand
Geraniol
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
Geraniol E122 3.37x37 TM3 polar (charge-assisted hydrogen bond)
Geraniol Y191 ECL2 hydrophobic
Geraniol Y191 ECL2 Van der Waals
Geraniol M207 5.42x43 TM5 hydrophobic
Geraniol M207 5.42x43 TM5 Van der Waals
Geraniol F208 5.43x44 TM5 hydrophobic
Geraniol F208 5.43x44 TM5 Van der Waals
Geraniol H211 5.46x461 TM5 Van der Waals
Geraniol H211 5.46x461 TM5 polar (hydrogen bond with backbone)
Geraniol F212 5.47x47 TM5 hydrophobic
Geraniol F212 5.47x47 TM5 Van der Waals
Geraniol W265 6.48x48 TM6 hydrophobic
Geraniol Y268 6.51x51 TM6 Van der Waals
Geraniol Y268 6.51x51 TM6 hydrophobic
Geraniol A269 6.52x52 TM6 hydrophobic
Geraniol A269 6.52x52 TM6 Van der Waals
Geraniol A272 6.55x55 TM6 hydrophobic
Geraniol A272 6.55x55 TM6 Van der Waals

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Snake plot — Download: PNG | SVG
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
3x37 3.37x37 E122
TM5
5x43 5.42x43 M207
5x44 5.43x44 F208
5x461 5.46x461 H211
5x47 5.47x47 F212
TM6
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x52 6.52x52 A269
6x55 6.55x55 A272