PDB
6LPB
Resolution
3.9 Å
Released
March 11, 2020
Receptor
PAC1
Class
B1
Species
Homo sapiens
Ligand
PACAP-38
Function
Agonist
Reference
10.1038/S41594-020-0386-8

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Ligand Amino Acid Generic Number Segment Interaction Type
PACAP-38 F27 N-term hydrophobic
PACAP-38 N60 N-term polar (hydrogen bond with backbone)
PACAP-38 N60 N-term Van der Waals
PACAP-38 I61 N-term hydrophobic
PACAP-38 I83 N-term Van der Waals
PACAP-38 I83 N-term hydrophobic
PACAP-38 Q146 1.32x32 TM1 Van der Waals
PACAP-38 Y150 1.36x36 TM1 polar (hydrogen bond)
PACAP-38 V153 1.39x39 TM1 Van der Waals
PACAP-38 V153 1.39x39 TM1 hydrophobic
PACAP-38 K154 1.40x40 TM1 polar (charge-assisted hydrogen bond)
PACAP-38 Y157 1.43x43 TM1 Van der Waals
PACAP-38 Y157 1.43x43 TM1 aromatic (edge-to-face)
PACAP-38 Y161 1.47x47 TM1 polar (hydrogen bond)
PACAP-38 V203 2.64x64 TM2 Van der Waals
PACAP-38 K206 2.67x67 TM2 polar (charge-assisted hydrogen bond)
PACAP-38 L210 2.71x71 TM2 polar (hydrogen bond with backbone)
PACAP-38 L210 2.71x71 TM2 Van der Waals
PACAP-38 Y211 2.72x72 TM2 aromatic (face-to-edge)
PACAP-38 Y211 2.72x72 TM2 Van der Waals
PACAP-38 F233 3.36x36 TM3 hydrophobic
PACAP-38 F233 3.36x36 TM3 Van der Waals
PACAP-38 V237 3.40x40 TM3 Van der Waals
PACAP-38 V237 3.40x40 TM3 hydrophobic
PACAP-38 Y241 3.44x44 TM3 Van der Waals
PACAP-38 D298 45.52x52 ECL2 polar (charge-assisted hydrogen bond)
PACAP-38 M299 ECL2 Van der Waals
PACAP-38 N300 ECL2 Van der Waals
PACAP-38 W306 5.36x37 TM5 aromatic (edge-to-face)
PACAP-38 W306 5.36x37 TM5 Van der Waals
PACAP-38 I309 5.39x39 TM5 Van der Waals
PACAP-38 K310 5.40x40 TM5 Van der Waals
PACAP-38 K378 7.35x34 TM7 Van der Waals
PACAP-38 R381 7.38x37 TM7 Van der Waals
PACAP-38 L382 7.39x38 TM7 Van der Waals
PACAP-38 L382 7.39x38 TM7 hydrophobic
PACAP-38 E385 7.42x41 TM7 polar (charge-assisted hydrogen bond)
PACAP-38 L386 7.43x42 TM7 Van der Waals
PACAP-38 L386 7.43x42 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(B)
PAC1 receptor
TM1
1x28 1.32x32 Q146
1x32 1.36x36 Y150
1x35 1.39x39 V153
1x36 1.40x40 K154
1x39 1.43x43 Y157
1x43 1.47x47 Y161
TM2
2x57 2.64x64 V203
2x60 2.67x67 K206
2x64 2.71x71 L210
TM3
3x32 3.36x36 F233
3x36 3.40x40 V237
3x40 3.44x44 Y241
ECL2
45x52 45.52x52 D298
TM5
5x41 5.36x37 W306
5x43 5.39x39 I309
5x44 5.40x40 K310
TM7
7x30 7.35x34 K378
7x33 7.38x37 R381
7x34 7.39x38 L382
7x37 7.42x41 E385
7x38 7.43x42 L386