PDB
9KWX
Resolution
3.1 Å
Released
Nov. 26, 2025
Receptor
C5a1
Class
A
Species
Mus musculus
Ligand
C5a-desArg
Function
Agonist
Reference
10.1101/2025.05.26.656101

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Ligand Amino Acid Generic Number Segment Interaction Type
C5a-desArg L92 2.60x60 TM2 hydrophobic
C5a-desArg N100 ECL1 Van der Waals
C5a-desArg N100 ECL1 polar (hydrogen bond)
C5a-desArg W102 23.50x50 ECL1 hydrophobic
C5a-desArg L117 3.33x33 TM3 Van der Waals
C5a-desArg L117 3.33x33 TM3 hydrophobic
C5a-desArg R175 4.64x65 TM4 polar (charge-assisted hydrogen bond)
C5a-desArg E176 ECL2 Van der Waals
C5a-desArg E176 ECL2 polar (hydrogen bond with backbone)
C5a-desArg Y178 ECL2 Van der Waals
C5a-desArg D180 ECL2 Van der Waals
C5a-desArg D180 ECL2 polar (hydrogen bond with backbone)
C5a-desArg F181 ECL2 Van der Waals
C5a-desArg F181 ECL2 hydrophobic
C5a-desArg V187 ECL2 hydrophobic
C5a-desArg V187 ECL2 Van der Waals
C5a-desArg C188 45.50x50 ECL2 Van der Waals
C5a-desArg G189 45.51x51 ECL2 Van der Waals
C5a-desArg I190 45.52x52 ECL2 polar (hydrogen bond with backbone)
C5a-desArg I190 45.52x52 ECL2 Van der Waals
C5a-desArg N191 ECL2 Van der Waals
C5a-desArg Y192 ECL2 polar (hydrogen bond with backbone)
C5a-desArg Y192 ECL2 Van der Waals
C5a-desArg G193 ECL2 Van der Waals
C5a-desArg Y259 6.51x51 TM6 polar (hydrogen bond)
C5a-desArg Y259 6.51x51 TM6 Van der Waals
C5a-desArg I266 6.58x58 TM6 polar (hydrogen bond with backbone)
C5a-desArg I266 6.58x58 TM6 Van der Waals
C5a-desArg N283 7.35x34 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
TM2
2x60 2.60x60 L92
ECL1
23x50 23.50x50 W102
TM3
3x33 3.33x33 L117
TM4
4x65 4.64x65 R175
ECL2
45x50 45.50x50 C188
45x51 45.51x51 G189
45x52 45.52x52 I190
TM6
6x51 6.51x51 Y259
6x58 6.58x58 I266
TM7
7x34 7.35x34 N283