PDB
8XYD
Resolution
2.9 Å
Released
Nov. 13, 2024
Receptor
PAF
Class
A
Species
Homo sapiens
Ligand
Function
PAF
Agonist
Reference
10.1016/J.CELREP.2024.114422

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Ligand Amino Acid Generic Number Segment Interaction Type
PAF Y22 1.39x39 TM1 Van der Waals
PAF W73 2.60x60 TM2 aromatic (pi-cation)
PAF Y77 2.64x64 TM2 Van der Waals
PAF F97 3.32x32 TM3 aromatic (pi-cation)
PAF F98 3.33x33 TM3 hydrophobic
PAF Y102 3.37x37 TM3 hydrophobic
PAF V105 3.40x40 TM3 hydrophobic
PAF A106 3.41x41 TM3 hydrophobic
PAF I145 4.53x53 TM4 Van der Waals
PAF A148 4.56x56 TM4 Van der Waals
PAF A149 4.57x57 TM4 Van der Waals
PAF F152 4.60x60 TM4 hydrophobic
PAF F174 45.51x51 ECL2 hydrophobic
PAF E175 45.52x52 ECL2 Van der Waals
PAF H176 ECL2 Van der Waals
PAF Y177 ECL2 hydrophobic
PAF V184 5.36x36 TM5 Van der Waals
PAF I187 5.39x39 TM5 hydrophobic
PAF H188 5.40x40 TM5 polar (hydrogen bond)
PAF F190 5.42x42 TM5 hydrophobic
PAF I191 5.43x43 TM5 hydrophobic
PAF S194 5.46x46 TM5 Van der Waals
PAF F195 5.47x47 TM5 Van der Waals
PAF V198 5.50x50 TM5 hydrophobic
PAF H248 6.51x51 TM6 Van der Waals
PAF W255 6.58x58 TM6 hydrophobic
PAF H275 7.35x34 TM7 polar (hydrogen bond)
PAF L279 7.39x38 TM7 Van der Waals

PAF

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

GPCRdb(A)
GPCRdb(A)
PAF receptor
TM1
1x39 1.39x39 Y22
TM2
2x60 2.60x60 W73
2x64 2.64x64 Y77
TM3
3x32 3.32x32 F97
3x33 3.33x33 F98
3x37 3.37x37 Y102
3x40 3.40x40 V105
3x41 3.41x41 A106
TM4
4x53 4.53x53 I145
4x56 4.56x56 A148
4x57 4.57x57 A149
4x60 4.60x60 F152
ECL2
45x51 45.51x51 F174
45x52 45.52x52 E175
TM5
5x36 5.36x36 V184
5x39 5.39x39 I187
5x40 5.40x40 H188
5x42 5.42x42 F190
5x43 5.43x43 I191
5x46 5.46x46 S194
5x47 5.47x47 F195
5x50 5.50x50 V198
TM6
6x51 6.51x51 H248
6x58 6.58x58 W255
TM7
7x34 7.35x34 H275
7x38 7.39x38 L279