PDB
9UMX
Resolution
3.2 Å
Released
Nov. 26, 2025
Receptor
C5a1
Class
A
Species
Homo sapiens
Ligand
EP54
Function
Agonist
Reference
10.1101/2025.05.26.656101

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Ligand Amino Acid Generic Number Segment Interaction Type
EP54 L92 2.60x60 TM2 hydrophobic
EP54 W102 23.50x50 ECL1 hydrophobic
EP54 P113 3.29x29 TM3 hydrophobic
EP54 R175 ECL2 polar (charge-assisted hydrogen bond)
EP54 R178 ECL2 Van der Waals
EP54 L187 ECL2 Van der Waals
EP54 C188 45.50x50 ECL2 polar (hydrogen bond with backbone)
EP54 C188 45.50x50 ECL2 Van der Waals
EP54 G189 45.51x51 ECL2 Van der Waals
EP54 V190 45.52x52 ECL2 polar (hydrogen bond with backbone)
EP54 V190 45.52x52 ECL2 Van der Waals
EP54 D191 ECL2 polar (charge-assisted hydrogen bond)
EP54 H194 ECL2 Van der Waals
EP54 D195 ECL2 polar (charge-assisted hydrogen bond)
EP54 Y258 6.51x51 TM6 Van der Waals
EP54 G262 6.55x55 TM6 Van der Waals
EP54 M265 6.58x58 TM6 Van der Waals
EP54 L268 6.61x61 TM6 polar (hydrogen bond with backbone)
EP54 L268 6.61x61 TM6 Van der Waals
EP54 E269 ECL3 Van der Waals
EP54 P270 ECL3 Van der Waals
EP54 F275 7.28x27 TM7 Van der Waals
EP54 D282 7.35x34 TM7 polar (charge-assisted hydrogen bond)

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

GPCRdb(A)
GPCRdb(A)
C5a1 receptor
TM2
2x60 2.60x60 L92
ECL1
23x50 23.50x50 W102
TM3
3x29 3.29x29 P113
ECL2
45x50 45.50x50 C188
45x51 45.51x51 G189
45x52 45.52x52 V190
TM6
6x51 6.51x51 Y258
6x55 6.55x55 G262
6x58 6.58x58 M265
6x61 6.61x61 L268
TM7
7x27 7.28x27 F275
7x34 7.35x34 D282