PDB
9V3C
Resolution
3.8 Å
Released
July 1, 2026
Receptor
C5a2
Class
A
Species
Homo sapiens
Ligand
[125I]C5a (human)
Function
Agonist
Reference
10.1016/J.MOLCEL.2026.06.002

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Ligand Amino Acid Generic Number Segment Interaction Type
[125I]C5a (human) V21 N-term polar (hydrogen bond with backbone)
[125I]C5a (human) V21 N-term Van der Waals
[125I]C5a (human) L24 N-term hydrophobic
[125I]C5a (human) D25 N-term Van der Waals
[125I]C5a (human) I89 2.59x59 TM2 Van der Waals
[125I]C5a (human) L90 2.60x60 TM2 hydrophobic
[125I]C5a (human) L90 2.60x60 TM2 Van der Waals
[125I]C5a (human) W100 23.50x50 ECL1 hydrophobic
[125I]C5a (human) W100 23.50x50 ECL1 Van der Waals
[125I]C5a (human) L110 3.28x28 TM3 hydrophobic
[125I]C5a (human) L110 3.28x28 TM3 Van der Waals
[125I]C5a (human) P111 3.29x29 TM3 Van der Waals
[125I]C5a (human) P111 3.29x29 TM3 hydrophobic
[125I]C5a (human) I114 3.32x32 TM3 Van der Waals
[125I]C5a (human) I114 3.32x32 TM3 hydrophobic
[125I]C5a (human) L115 3.33x33 TM3 Van der Waals
[125I]C5a (human) L115 3.33x33 TM3 hydrophobic
[125I]C5a (human) S169 4.60x61 TM4 polar (hydrogen bond)
[125I]C5a (human) S169 4.60x61 TM4 Van der Waals
[125I]C5a (human) R173 ECL2 polar (charge-assisted hydrogen bond)
[125I]C5a (human) R174 ECL2 Van der Waals
[125I]C5a (human) H176 ECL2 polar (hydrogen bond)
[125I]C5a (human) H179 ECL2 Van der Waals
[125I]C5a (human) F180 ECL2 Van der Waals
[125I]C5a (human) F180 ECL2 hydrophobic
[125I]C5a (human) V187 45.51x51 ECL2 hydrophobic
[125I]C5a (human) V187 45.51x51 ECL2 Van der Waals
[125I]C5a (human) V188 45.52x52 ECL2 polar (hydrogen bond with backbone)
[125I]C5a (human) V188 45.52x52 ECL2 Van der Waals
[125I]C5a (human) E197 5.35x36 TM5 polar (charge-assisted hydrogen bond)
[125I]C5a (human) Y249 6.51x51 TM6 hydrophobic
[125I]C5a (human) Y249 6.51x51 TM6 Van der Waals
[125I]C5a (human) L252 6.54x54 TM6 Van der Waals
[125I]C5a (human) G253 6.55x55 TM6 polar (hydrogen bond with backbone)
[125I]C5a (human) G253 6.55x55 TM6 Van der Waals
[125I]C5a (human) L256 6.58x58 TM6 Van der Waals
[125I]C5a (human) T257 6.59x59 TM6 Van der Waals
[125I]C5a (human) T257 6.59x59 TM6 polar (hydrogen bond with backbone)
[125I]C5a (human) A259 6.61x61 TM6 polar (hydrogen bond with backbone)
[125I]C5a (human) A259 6.61x61 TM6 Van der Waals
[125I]C5a (human) P261 ECL3 Van der Waals
[125I]C5a (human) P261 ECL3 hydrophobic
[125I]C5a (human) N262 ECL3 Van der Waals
[125I]C5a (human) A264 7.26x25 TM7 Van der Waals
[125I]C5a (human) A267 7.29x28 TM7 Van der Waals
[125I]C5a (human) L270 7.32x31 TM7 hydrophobic
[125I]C5a (human) L270 7.32x31 TM7 Van der Waals
[125I]C5a (human) E273 7.35x34 TM7 polar (charge-assisted hydrogen bond)

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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
2x59 2.59x59 I89
2x60 2.60x60 L90
ECL1
23x50 23.50x50 W100
TM3
3x28 3.28x28 L110
3x29 3.29x29 P111
3x32 3.32x32 I114
3x33 3.33x33 L115
TM4
4x61 4.60x61 S169
ECL2
45x51 45.51x51 V187
45x52 45.52x52 V188
TM5
5x36 5.35x36 E197
TM6
6x51 6.51x51 Y249
6x54 6.54x54 L252
6x55 6.55x55 G253
6x58 6.58x58 L256
6x59 6.59x59 T257
6x61 6.61x61 A259
TM7
7x25 7.26x25 A264
7x28 7.29x28 A267
7x31 7.32x31 L270
7x34 7.35x34 E273