PDB
8QOT
Resolution
3.2 Å
Released
Dec. 27, 2023
Receptor
μ
Class
A
Species
Mus musculus
Ligand
Function
Nanobody E (NbE)
Antagonist
Reference
10.1101/2023.12.06.570395

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Ligand Amino Acid Generic Number Segment Interaction Type
Nanobody E (NbE) I144 3.29x29 TM3 Van der Waals
Nanobody E (NbE) D147 3.32x32 TM3 hydrophobic
Nanobody E (NbE) Y148 3.33x33 TM3 aromatic (edge-to-face)
Nanobody E (NbE) Y148 3.33x33 TM3 hydrophobic
Nanobody E (NbE) Y148 3.33x33 TM3 polar (hydrogen bond)
Nanobody E (NbE) M151 3.36x36 TM3 hydrophobic
Nanobody E (NbE) K209 ECL2 polar (charge-charge)
Nanobody E (NbE) K209 ECL2 polar (hydrogen bond)
Nanobody E (NbE) R211 ECL2 polar (hydrogen bond)
Nanobody E (NbE) R211 ECL2 polar (charge-charge)
Nanobody E (NbE) R211 ECL2 hydrophobic
Nanobody E (NbE) Q212 ECL2 Van der Waals
Nanobody E (NbE) T218 45.51x51 ECL2 Van der Waals
Nanobody E (NbE) L219 45.52x52 ECL2 hydrophobic
Nanobody E (NbE) F221 ECL2 Van der Waals
Nanobody E (NbE) E229 5.35x36 TM5 polar (hydrogen bond)
Nanobody E (NbE) L232 5.38x39 TM5 Van der Waals
Nanobody E (NbE) K233 5.39x40 TM5 polar (hydrogen bond)
Nanobody E (NbE) V236 5.42x43 TM5 Van der Waals
Nanobody E (NbE) F237 5.43x44 TM5 Van der Waals
Nanobody E (NbE) W293 6.48x48 TM6 hydrophobic
Nanobody E (NbE) I296 6.51x51 TM6 Van der Waals
Nanobody E (NbE) H297 6.52x52 TM6 polar (hydrogen bond)
Nanobody E (NbE) Y299 6.54x54 TM6 Van der Waals
Nanobody E (NbE) V300 6.55x55 TM6 hydrophobic
Nanobody E (NbE) K303 6.58x58 TM6 Van der Waals
Nanobody E (NbE) P309 ECL3 Van der Waals
Nanobody E (NbE) E310 ECL3 polar (hydrogen bond)
Nanobody E (NbE) W318 7.35x34 TM7 Van der Waals
Nanobody E (NbE) I322 7.39x38 TM7 hydrophobic
Nanobody E (NbE) Y326 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
μ receptor
TM3
3x29 3.29x29 I144
3x32 3.32x32 D147
3x33 3.33x33 Y148
3x36 3.36x36 M151
ECL2
45x51 45.51x51 T218
45x52 45.52x52 L219
TM5
5x36 5.35x36 E229
5x39 5.38x39 L232
5x40 5.39x40 K233
5x43 5.42x43 V236
5x44 5.43x44 F237
TM6
6x48 6.48x48 W293
6x51 6.51x51 I296
6x52 6.52x52 H297
6x54 6.54x54 Y299
6x55 6.55x55 V300
6x58 6.58x58 K303
TM7
7x34 7.35x34 W318
7x38 7.39x38 I322
7x42 7.43x42 Y326