PDB
6FKD
Resolution
2.5 Å
Released
April 4, 2018
Receptor
Rhodopsin
Class
A
Species
Bos taurus
Ligand
RS16
Function
Agonist
Reference
10.1073/PNAS.1718084115

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Ligand Amino Acid Generic Number Segment Interaction Type
RS16 L125 3.40x40 TM3 hydrophobic
RS16 Y191 ECL2 hydrophobic
RS16 M207 5.42x43 TM5 hydrophobic
RS16 F208 5.43x44 TM5 hydrophobic
RS16 H211 5.46x461 TM5 Van der Waals
RS16 H211 5.46x461 TM5 polar (hydrogen bond with backbone)
RS16 F212 5.47x47 TM5 hydrophobic
RS16 F212 5.47x47 TM5 Van der Waals
RS16 F261 6.44x44 TM6 Van der Waals
RS16 F261 6.44x44 TM6 hydrophobic
RS16 C264 6.47x47 TM6 Van der Waals
RS16 W265 6.48x48 TM6 Van der Waals
RS16 W265 6.48x48 TM6 hydrophobic
RS16 Y268 6.51x51 TM6 hydrophobic
RS16 Y268 6.51x51 TM6 Van der Waals
RS16 A272 6.55x55 TM6 hydrophobic
RS16 A272 6.55x55 TM6 Van der Waals
RS16 M288 ECL3 Van der Waals
RS16 M288 ECL3 hydrophobic

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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
3x40 3.40x40 L125
TM5
5x43 5.42x43 M207
5x44 5.43x44 F208
5x461 5.46x461 H211
5x47 5.47x47 F212
TM6
6x44 6.44x44 F261
6x47 6.47x47 C264
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x55 6.55x55 A272