PDB
7YM8
Resolution
2.9 Å
Released
July 5, 2023
Receptor
α1A
Class
A
Species
Homo sapiens
Ligands
Function
Nanobody 29 (Nb29)
PAM
oxymetazoline
Agonist (partial)
Reference
10.1038/S41467-023-39310-X
Nanobody 29 (Nb29) oxymetazoline

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Ligand Amino Acid Generic Number Segment Interaction Type
Nanobody 29 (Nb29) F86 2.64x63 TM2 hydrophobic
Nanobody 29 (Nb29) L89 2.67x66 TM2 Van der Waals
Nanobody 29 (Nb29) G90 2.68x67 TM2 Van der Waals
Nanobody 29 (Nb29) Y91 23.49x49 ECL1 hydrophobic
oxymetazoline D106 3.32x32 TM3 polar (charge-charge)
oxymetazoline D106 3.32x32 TM3 polar (hydrogen bond)
oxymetazoline V107 3.33x33 TM3 hydrophobic
oxymetazoline C110 3.36x36 TM3 hydrophobic
Nanobody 29 (Nb29) R166 ECL2 polar (hydrogen bond)
Nanobody 29 (Nb29) R166 ECL2 polar (charge-charge)
Nanobody 29 (Nb29) Q167 ECL2 Van der Waals
Nanobody 29 (Nb29) P170 ECL2 hydrophobic
Nanobody 29 (Nb29) E171 ECL2 polar (charge-charge)
Nanobody 29 (Nb29) E171 ECL2 polar (hydrogen bond)
Nanobody 29 (Nb29) D172 ECL2 polar (charge-charge)
Nanobody 29 (Nb29) D172 ECL2 polar (hydrogen bond)
Nanobody 29 (Nb29) D172 ECL2 polar (hydrogen bond with backbone)
Nanobody 29 (Nb29) D172 ECL2 hydrophobic
Nanobody 29 (Nb29) T174 ECL2 polar (hydrogen bond)
Nanobody 29 (Nb29) I175 ECL2 hydrophobic
Nanobody 29 (Nb29) C176 45.50x50 ECL2 polar (hydrogen bond with backbone)
Nanobody 29 (Nb29) Q177 45.51x51 ECL2 polar (hydrogen bond)
Nanobody 29 (Nb29) I178 45.52x52 ECL2 Van der Waals
oxymetazoline I178 45.52x52 ECL2 Van der Waals
oxymetazoline N179 ECL2 Van der Waals
Nanobody 29 (Nb29) E180 ECL2 hydrophobic
Nanobody 29 (Nb29) E180 ECL2 polar (charge-charge)
oxymetazoline Y184 5.38x39 TM5 hydrophobic
oxymetazoline V185 5.39x40 TM5 hydrophobic
oxymetazoline S188 5.42x43 TM5 Van der Waals
oxymetazoline W285 6.48x48 TM6 Van der Waals
oxymetazoline F288 6.51x51 TM6 hydrophobic
oxymetazoline F288 6.51x51 TM6 aromatic (pi-cation)
oxymetazoline F288 6.51x51 TM6 aromatic (edge-to-face)
oxymetazoline F289 6.52x52 TM6 Van der Waals
oxymetazoline M292 6.55x55 TM6 hydrophobic
Nanobody 29 (Nb29) K302 ECL3 Van der Waals
Nanobody 29 (Nb29) E305 7.32x31 TM7 polar (charge-charge)
Nanobody 29 (Nb29) E305 7.32x31 TM7 polar (hydrogen bond)
Nanobody 29 (Nb29) F308 7.35x34 TM7 aromatic (pi-cation)
Nanobody 29 (Nb29) F308 7.35x34 TM7 hydrophobic
Nanobody 29 (Nb29) K309 7.36x35 TM7 aromatic (pi-cation)
oxymetazoline F312 7.39x38 TM7 hydrophobic
oxymetazoline F312 7.39x38 TM7 aromatic (pi-cation)
oxymetazoline G315 7.42x41 TM7 Van der Waals
oxymetazoline Y316 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
α1A-adrenoceptor
TM2
2x63 2.64x63 F86
2x66 2.67x66 L89
2x67 2.68x67 G90
ECL1
23x49 23.49x49 Y91
TM3
3x32 3.32x32 D106
3x33 3.33x33 V107
3x36 3.36x36 C110
ECL2
45x50 45.50x50 C176
45x51 45.51x51 Q177
45x52 45.52x52 I178
TM5
5x39 5.38x39 Y184
5x40 5.39x40 V185
5x43 5.42x43 S188
TM6
6x48 6.48x48 W285
6x51 6.51x51 F288
6x52 6.52x52 F289
6x55 6.55x55 M292
TM7
7x31 7.32x31 E305
7x34 7.35x34 F308
7x35 7.36x35 K309
7x38 7.39x38 F312
7x41 7.42x41 G315
7x42 7.43x42 Y316