PDB
9V3Y
Resolution
3.1 Å
Released
July 1, 2026
Receptor
C5a2
Class
A
Species
Homo sapiens
Ligand
C5a-pep
Function
Agonist
Reference
10.1016/J.MOLCEL.2026.06.002

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Ligand Amino Acid Generic Number Segment Interaction Type
C5a-pep L90 2.60x60 TM2 hydrophobic
C5a-pep W100 23.50x50 ECL1 hydrophobic
C5a-pep P111 3.29x29 TM3 hydrophobic
C5a-pep I114 3.32x32 TM3 hydrophobic
C5a-pep L115 3.33x33 TM3 hydrophobic
C5a-pep R173 ECL2 polar (charge-assisted hydrogen bond)
C5a-pep H176 ECL2 Van der Waals
C5a-pep Q185 ECL2 Van der Waals
C5a-pep C186 45.50x50 ECL2 Van der Waals
C5a-pep C186 45.50x50 ECL2 polar (hydrogen bond with backbone)
C5a-pep V187 45.51x51 ECL2 Van der Waals
C5a-pep V187 45.51x51 ECL2 hydrophobic
C5a-pep V188 45.52x52 ECL2 polar (hydrogen bond with backbone)
C5a-pep V188 45.52x52 ECL2 Van der Waals
C5a-pep D189 ECL2 Van der Waals
C5a-pep T201 5.39x40 TM5 Van der Waals
C5a-pep R204 5.42x43 TM5 polar (charge-assisted hydrogen bond)
C5a-pep Y249 6.51x51 TM6 hydrophobic
C5a-pep Y249 6.51x51 TM6 Van der Waals
C5a-pep G253 6.55x55 TM6 Van der Waals
C5a-pep L256 6.58x58 TM6 Van der Waals
C5a-pep E273 7.35x34 TM7 polar (charge-assisted hydrogen bond)
C5a-pep V277 7.39x38 TM7 hydrophobic
C5a-pep V277 7.39x38 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
C5a2 receptor
TM2
2x60 2.60x60 L90
ECL1
23x50 23.50x50 W100
TM3
3x29 3.29x29 P111
3x32 3.32x32 I114
3x33 3.33x33 L115
ECL2
45x50 45.50x50 C186
45x51 45.51x51 V187
45x52 45.52x52 V188
TM5
5x40 5.39x40 T201
5x43 5.42x43 R204
TM6
6x51 6.51x51 Y249
6x55 6.55x55 G253
6x58 6.58x58 L256
TM7
7x34 7.35x34 E273
7x38 7.39x38 V277