PDB
9KWG
Resolution
3.2 Å
Released
Nov. 26, 2025
Receptor
C5a1
Class
A
Species
Mus musculus
Ligand
C5A
Function
Agonist
Reference
10.1101/2025.05.26.656101

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Ligand Amino Acid Generic Number Segment Interaction Type
C5A P24 N-term hydrophobic
C5A A25 N-term Van der Waals
C5A A25 N-term polar (hydrogen bond with backbone)
C5A D26 N-term Van der Waals
C5A I28 N-term Van der Waals
C5A I28 N-term hydrophobic
C5A L30 N-term Van der Waals
C5A K32 N-term Van der Waals
C5A L92 2.60x60 TM2 Van der Waals
C5A L92 2.60x60 TM2 hydrophobic
C5A V96 2.64x64 TM2 Van der Waals
C5A N100 ECL1 polar (hydrogen bond)
C5A N100 ECL1 polar (hydrogen bond)
C5A N100 ECL1 Van der Waals
C5A W102 23.50x50 ECL1 hydrophobic
C5A W102 23.50x50 ECL1 Van der Waals
C5A P113 3.29x29 TM3 hydrophobic
C5A P113 3.29x29 TM3 Van der Waals
C5A I116 3.32x32 TM3 hydrophobic
C5A I116 3.32x32 TM3 Van der Waals
C5A L117 3.33x33 TM3 Van der Waals
C5A L117 3.33x33 TM3 hydrophobic
C5A M120 3.36x36 TM3 Van der Waals
C5A R175 4.64x65 TM4 polar (charge-assisted hydrogen bond)
C5A E176 ECL2 Van der Waals
C5A D180 ECL2 polar (charge-assisted hydrogen bond)
C5A D180 ECL2 polar (hydrogen bond with backbone)
C5A F181 ECL2 Van der Waals
C5A F181 ECL2 hydrophobic
C5A V187 ECL2 hydrophobic
C5A V187 ECL2 Van der Waals
C5A C188 45.50x50 ECL2 Van der Waals
C5A G189 45.51x51 ECL2 Van der Waals
C5A I190 45.52x52 ECL2 Van der Waals
C5A I190 45.52x52 ECL2 hydrophobic
C5A N191 ECL2 Van der Waals
C5A Y259 6.51x51 TM6 polar (hydrogen bond)
C5A Y259 6.51x51 TM6 polar (hydrogen bond with backbone)
C5A Y259 6.51x51 TM6 Van der Waals
C5A T262 6.54x54 TM6 polar (hydrogen bond)
C5A T262 6.54x54 TM6 Van der Waals
C5A G263 6.55x55 TM6 Van der Waals
C5A I266 6.58x58 TM6 Van der Waals
C5A N283 7.35x34 TM7 polar (hydrogen bond)
C5A N283 7.35x34 TM7 Van der Waals
C5A S284 7.36x35 TM7 polar (hydrogen bond)
C5A S284 7.36x35 TM7 polar (hydrogen bond)
C5A S284 7.36x35 TM7 Van der Waals

C5A

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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
2x64 2.64x64 V96
ECL1
23x50 23.50x50 W102
TM3
3x29 3.29x29 P113
3x32 3.32x32 I116
3x33 3.33x33 L117
3x36 3.36x36 M120
TM4
4x65 4.64x65 R175
ECL2
45x50 45.50x50 C188
45x51 45.51x51 G189
45x52 45.52x52 I190
TM6
6x51 6.51x51 Y259
6x54 6.54x54 T262
6x55 6.55x55 G263
6x58 6.58x58 I266
TM7
7x34 7.35x34 N283
7x35 7.36x35 S284