PDB
8GDC
Resolution
3.5 Å
Released
Jan. 10, 2024
Receptor
EP3
Class
A
Species
Homo sapiens
Ligand
PGE2
Function
Agonist
Reference
10.1073/PNAS.2216329120

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Ligand Amino Acid Generic Number Segment Interaction Type
PGE2 P55 1.39x39 TM1 hydrophobic
PGE2 M58 1.42x42 TM1 polar (hydrogen bond)
PGE2 G102 2.53x53 TM2 Van der Waals
PGE2 G102 2.53x53 TM2 polar (hydrogen bond with backbone)
PGE2 Q103 2.54x54 TM2 polar (hydrogen bond)
PGE2 Q103 2.54x54 TM2 Van der Waals
PGE2 T107 2.58x58 TM2 Van der Waals
PGE2 M137 3.32x32 TM3 hydrophobic
PGE2 M137 3.32x32 TM3 Van der Waals
PGE2 G141 3.36x36 TM3 Van der Waals
PGE2 W207 ECL2 hydrophobic
PGE2 W207 ECL2 Van der Waals
PGE2 F209 45.51x51 ECL2 hydrophobic
PGE2 W295 6.48x48 TM6 Van der Waals
PGE2 W295 6.48x48 TM6 hydrophobic
PGE2 R333 7.40x39 TM7 polar (charge-assisted hydrogen bond)
PGE2 S336 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
EP3 receptor
TM1
1x39 1.39x39 P55
1x42 1.42x42 M58
TM2
2x53 2.53x53 G102
2x54 2.54x54 Q103
2x58 2.58x58 T107
TM3
3x32 3.32x32 M137
3x36 3.36x36 G141
ECL2
45x51 45.51x51 F209
TM6
6x48 6.48x48 W295
TM7
7x39 7.40x39 R333
7x42 7.43x42 S336