PDB
7C4S
Resolution
3.2 Å
Released
June 9, 2021
Receptor
S1P3
Class
A
Species
Homo sapiens
Ligand
Function
sphingosine 1-phosphate
Agonist
Reference
10.1126/SCIADV.ABF5325

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Ligand Amino Acid Generic Number Segment Interaction Type
sphingosine 1-phosphate Y22 N-term polar (hydrogen bond)
sphingosine 1-phosphate K27 N-term polar (charge-charge)
sphingosine 1-phosphate E37 N-term polar (hydrogen bond)
sphingosine 1-phosphate N95 2.60x60 TM2 polar (hydrogen bond)
sphingosine 1-phosphate S99 2.64x64 TM2 polar (hydrogen bond)
sphingosine 1-phosphate G100 23.47x47 ECL1 polar (hydrogen bond with backbone)
sphingosine 1-phosphate T103 23.50x50 ECL1 Van der Waals
sphingosine 1-phosphate R114 3.28x28 TM3 polar (charge-charge)
sphingosine 1-phosphate E115 3.29x29 TM3 polar (charge-charge)
sphingosine 1-phosphate E115 3.29x29 TM3 polar (hydrogen bond)
sphingosine 1-phosphate M118 3.32x32 TM3 Van der Waals
sphingosine 1-phosphate F119 3.33x33 TM3 hydrophobic
sphingosine 1-phosphate L122 3.36x36 TM3 hydrophobic
sphingosine 1-phosphate T126 3.40x40 TM3 Van der Waals
sphingosine 1-phosphate L168 4.56x56 TM4 hydrophobic
sphingosine 1-phosphate I203 5.46x46 TM5 hydrophobic
sphingosine 1-phosphate F204 5.47x47 TM5 Van der Waals
sphingosine 1-phosphate W256 6.48x48 TM6 hydrophobic
sphingosine 1-phosphate L259 6.51x51 TM6 Van der Waals
sphingosine 1-phosphate F260 6.52x52 TM6 hydrophobic
sphingosine 1-phosphate F263 6.55x55 TM6 Van der Waals
sphingosine 1-phosphate I284 7.39x38 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
S1P3 receptor
TM2
2x60 2.60x60 N95
2x64 2.64x64 S99
ECL1
23x47 23.47x47 G100
23x50 23.50x50 T103
TM3
3x28 3.28x28 R114
3x29 3.29x29 E115
3x32 3.32x32 M118
3x33 3.33x33 F119
3x36 3.36x36 L122
3x40 3.40x40 T126
TM4
4x56 4.56x56 L168
TM5
5x46 5.46x46 I203
5x47 5.47x47 F204
TM6
6x48 6.48x48 W256
6x51 6.51x51 L259
6x52 6.52x52 F260
6x55 6.55x55 F263
TM7
7x38 7.39x38 I284