PDB
8FD0
Resolution
3.7 Å
Released
Aug. 30, 2023
Receptor
Rhodopsin
Class
A
Species
Bos taurus
Ligand
Nanobody Nb2
Function
Allosteric antagonist
Reference
10.1038/S41467-023-40911-9

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Ligand Amino Acid Generic Number Segment Interaction Type
Nanobody Nb2 M1 N-term hydrophobic
Nanobody Nb2 P7 N-term Van der Waals
Nanobody Nb2 P7 N-term polar (hydrogen bond with backbone)
Nanobody Nb2 P194 ECL2 Van der Waals
Nanobody Nb2 P194 ECL2 hydrophobic
Nanobody Nb2 E196 ECL2 Van der Waals
Nanobody Nb2 E201 5.36x37 TM5 polar (charge-assisted hydrogen bond)
Nanobody Nb2 G280 ECL3 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
TM5
5x37 5.36x37 E201