PDB
9KX6
Resolution
3.1 Å
Released
Nov. 26, 2025
Receptor
C5a1
Class
A
Species
Mus musculus
Ligand
C5a des-Arg (Human)
Function
Agonist
Reference
10.1101/2025.05.26.656101

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Ligand Amino Acid Generic Number Segment Interaction Type
C5a des-Arg (Human) N100 ECL1 Van der Waals
C5a des-Arg (Human) N100 ECL1 polar (hydrogen bond)
C5a des-Arg (Human) I116 3.32x32 TM3 hydrophobic
C5a des-Arg (Human) I116 3.32x32 TM3 Van der Waals
C5a des-Arg (Human) L117 3.33x33 TM3 Van der Waals
C5a des-Arg (Human) L117 3.33x33 TM3 hydrophobic
C5a des-Arg (Human) M120 3.36x36 TM3 Van der Waals
C5a des-Arg (Human) R175 ECL2 polar (charge-assisted hydrogen bond)
C5a des-Arg (Human) D180 ECL2 Van der Waals
C5a des-Arg (Human) F181 ECL2 Van der Waals
C5a des-Arg (Human) F181 ECL2 hydrophobic
C5a des-Arg (Human) V187 ECL2 Van der Waals
C5a des-Arg (Human) G189 45.51x51 ECL2 Van der Waals
C5a des-Arg (Human) I190 45.52x52 ECL2 polar (hydrogen bond with backbone)
C5a des-Arg (Human) I190 45.52x52 ECL2 Van der Waals
C5a des-Arg (Human) Y192 ECL2 Van der Waals
C5a des-Arg (Human) Y192 ECL2 hydrophobic
C5a des-Arg (Human) R207 5.42x43 TM5 polar (charge-assisted hydrogen bond)
C5a des-Arg (Human) Y259 6.51x51 TM6 polar (hydrogen bond)
C5a des-Arg (Human) Y259 6.51x51 TM6 Van der Waals
C5a des-Arg (Human) I266 6.58x58 TM6 Van der Waals
C5a des-Arg (Human) I266 6.58x58 TM6 polar (hydrogen bond with backbone)
C5a des-Arg (Human) A267 6.59x59 TM6 Van der Waals
C5a des-Arg (Human) L269 6.61x61 TM6 polar (hydrogen bond with backbone)
C5a des-Arg (Human) L269 6.61x61 TM6 Van der Waals
C5a des-Arg (Human) S273 ECL3 polar (hydrogen bond with backbone)
C5a des-Arg (Human) S273 ECL3 polar (hydrogen bond)
C5a des-Arg (Human) N283 7.35x34 TM7 Van der Waals
C5a des-Arg (Human) N283 7.35x34 TM7 polar (hydrogen bond)
C5a des-Arg (Human) V287 7.39x38 TM7 hydrophobic
C5a des-Arg (Human) V287 7.39x38 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
C5a1 receptor
TM3
3x32 3.32x32 I116
3x33 3.33x33 L117
3x36 3.36x36 M120
ECL2
45x51 45.51x51 G189
45x52 45.52x52 I190
TM5
5x43 5.42x43 R207
TM6
6x51 6.51x51 Y259
6x58 6.58x58 I266
6x59 6.59x59 A267
6x61 6.61x61 L269
TM7
7x34 7.35x34 N283
7x38 7.39x38 V287