PDB
9UMR
Resolution
3.2 Å
Released
Nov. 26, 2025
Receptor
C5a1
Class
A
Species
Homo sapiens
Ligand
C5a-pep
Function
Agonist
Reference
10.1101/2025.05.26.656101

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Ligand Amino Acid Generic Number Segment Interaction Type
C5a-pep L92 2.60x60 TM2 hydrophobic
C5a-pep I116 3.32x32 TM3 hydrophobic
C5a-pep L117 3.33x33 TM3 hydrophobic
C5a-pep R175 ECL2 polar (charge-assisted hydrogen bond)
C5a-pep R178 ECL2 Van der Waals
C5a-pep L187 ECL2 Van der Waals
C5a-pep L187 ECL2 hydrophobic
C5a-pep C188 45.50x50 ECL2 Van der Waals
C5a-pep G189 45.51x51 ECL2 Van der Waals
C5a-pep V190 45.52x52 ECL2 polar (hydrogen bond with backbone)
C5a-pep V190 45.52x52 ECL2 Van der Waals
C5a-pep D191 ECL2 Van der Waals
C5a-pep R206 5.42x43 TM5 polar (charge-assisted hydrogen bond)
C5a-pep Y258 6.51x51 TM6 hydrophobic
C5a-pep Y258 6.51x51 TM6 Van der Waals
C5a-pep G262 6.55x55 TM6 Van der Waals
C5a-pep M265 6.58x58 TM6 polar (hydrogen bond with backbone)
C5a-pep M265 6.58x58 TM6 Van der Waals
C5a-pep S266 6.59x59 TM6 Van der Waals
C5a-pep F275 7.28x27 TM7 hydrophobic
C5a-pep F275 7.28x27 TM7 Van der Waals
C5a-pep K279 7.32x31 TM7 polar (charge-assisted hydrogen bond)
C5a-pep 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
TM3
3x32 3.32x32 I116
3x33 3.33x33 L117
ECL2
45x50 45.50x50 C188
45x51 45.51x51 G189
45x52 45.52x52 V190
TM5
5x43 5.42x43 R206
TM6
6x51 6.51x51 Y258
6x55 6.55x55 G262
6x58 6.58x58 M265
6x59 6.59x59 S266
TM7
7x27 7.28x27 F275
7x31 7.32x31 K279
7x34 7.35x34 D282