PDB
5JQH
Resolution
3.2 Å
Released
July 13, 2016
Receptor
β2
Class
A
Species
Homo sapiens
Ligands
Nanobody 60
(S)-carazolol
Function
NAM
Inverse agonist
Reference
10.1038/NATURE18636
Nanobody 60 (S)-carazolol

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Ligand Amino Acid Generic Number Segment Interaction Type
Nanobody 60 R1063 12.49x49 ICL1 Van der Waals
Nanobody 60 R1063 12.49x49 ICL1 polar (hydrogen bond with backbone)
Nanobody 60 L1064 12.50x50 ICL1 Van der Waals
Nanobody 60 L1064 12.50x50 ICL1 hydrophobic
Nanobody 60 T1066 2.37x37 TM2 polar (hydrogen bond)
Nanobody 60 T1066 2.37x37 TM2 Van der Waals
Nanobody 60 T1068 2.39x39 TM2 Van der Waals
Nanobody 60 N1069 2.40x40 TM2 polar (hydrogen bond)
Nanobody 60 N1069 2.40x40 TM2 Van der Waals
Nanobody 60 I1072 2.43x43 TM2 Van der Waals
Nanobody 60 I1072 2.43x43 TM2 hydrophobic
(S)-carazolol W1109 3.28x28 TM3 hydrophobic
(S)-carazolol D1113 3.32x32 TM3 polar (charge-assisted hydrogen bond)
(S)-carazolol V1114 3.33x33 TM3 Van der Waals
(S)-carazolol V1114 3.33x33 TM3 hydrophobic
(S)-carazolol V1117 3.36x36 TM3 hydrophobic
Nanobody 60 R1131 3.50x50 TM3 polar (charge-assisted hydrogen bond)
Nanobody 60 P1138 ICL2 Van der Waals
Nanobody 60 F1139 ICL2 hydrophobic
Nanobody 60 F1139 ICL2 Van der Waals
Nanobody 60 Y1141 ICL2 Van der Waals
Nanobody 60 Q1142 ICL2 polar (hydrogen bond)
Nanobody 60 Q1142 ICL2 polar (hydrogen bond)
Nanobody 60 Q1142 ICL2 polar (hydrogen bond)
Nanobody 60 L1144 ICL2 Van der Waals
Nanobody 60 L1144 ICL2 hydrophobic
Nanobody 60 L1145 ICL2 Van der Waals
(S)-carazolol F1193 45.52x52 ECL2 Van der Waals
(S)-carazolol F1193 45.52x52 ECL2 aromatic (edge-to-face)
(S)-carazolol A1200 5.39x40 TM5 Van der Waals
(S)-carazolol A1200 5.39x40 TM5 hydrophobic
(S)-carazolol S1203 5.42x43 TM5 Van der Waals
(S)-carazolol S1203 5.42x43 TM5 polar (hydrogen bond)
(S)-carazolol S1204 5.43x44 TM5 Van der Waals
Nanobody 60 F1264 ICL3 aromatic (edge-to-face)
Nanobody 60 F1264 ICL3 Van der Waals
Nanobody 60 K1267 ICL3 Van der Waals
Nanobody 60 E1268 ICL3 polar (charge-assisted hydrogen bond)
Nanobody 60 A1271 6.33x33 TM6 Van der Waals
Nanobody 60 A1271 6.33x33 TM6 hydrophobic
Nanobody 60 T1274 6.36x36 TM6 Van der Waals
Nanobody 60 L1275 6.37x37 TM6 Van der Waals
Nanobody 60 L1275 6.37x37 TM6 hydrophobic
(S)-carazolol W1286 6.48x48 TM6 Van der Waals
(S)-carazolol F1289 6.51x51 TM6 hydrophobic
(S)-carazolol F1289 6.51x51 TM6 Van der Waals
(S)-carazolol F1290 6.52x52 TM6 Van der Waals
(S)-carazolol F1290 6.52x52 TM6 aromatic (edge-to-face)
(S)-carazolol N1293 6.55x55 TM6 Van der Waals
(S)-carazolol N1312 7.39x38 TM7 polar (hydrogen bond)
(S)-carazolol N1312 7.39x38 TM7 polar (hydrogen bond)
(S)-carazolol N1312 7.39x38 TM7 Van der Waals
(S)-carazolol Y1316 7.43x42 TM7 Van der Waals
Nanobody 60 S1329 8.47x47 H8 Van der Waals
Nanobody 60 D1331 8.49x49 H8 polar (charge-assisted hydrogen bond)
Nanobody 60 F1332 8.50x50 H8 Van der Waals
Nanobody 60 F1332 8.50x50 H8 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
β2-adrenoceptor
ICL1
12x49 12.49x49 R63
12x50 12.50x50 L64
TM2
2x37 2.37x37 T66
2x39 2.39x39 T68
2x40 2.40x40 N69
2x43 2.43x43 I72
TM3
3x28 3.28x28 W109
3x32 3.32x32 D113
3x33 3.33x33 V114
3x36 3.36x36 V117
3x50 3.50x50 R131
ECL2
45x52 45.52x52 F193
TM5
5x40 5.39x40 A200
5x43 5.42x43 S203
5x44 5.43x44 S204
TM6
6x33 6.33x33 A271
6x36 6.36x36 T274
6x37 6.37x37 L275
6x48 6.48x48 W286
6x51 6.51x51 F289
6x52 6.52x52 F290
6x55 6.55x55 N293
TM7
7x38 7.39x38 N312
7x42 7.43x42 Y316
H8
8x47 8.47x47 S329
8x49 8.49x49 D331
8x50 8.50x50 F332