PDB
8JZP
Resolution
3.5 Å
Released
Jan. 15, 2025
Receptor
C5a1
Class
A
Species
Homo sapiens
Ligand
C5a anaphylatoxin
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
C5a anaphylatoxin D27 N-term polar (charge-assisted hydrogen bond)
C5a anaphylatoxin K28 N-term Van der Waals
C5a anaphylatoxin L92 2.60x60 TM2 Van der Waals
C5a anaphylatoxin L92 2.60x60 TM2 hydrophobic
C5a anaphylatoxin S95 2.63x63 TM2 polar (hydrogen bond)
C5a anaphylatoxin S95 2.63x63 TM2 Van der Waals
C5a anaphylatoxin H100 ECL1 Van der Waals
C5a anaphylatoxin W102 23.50x50 ECL1 Van der Waals
C5a anaphylatoxin W102 23.50x50 ECL1 hydrophobic
C5a anaphylatoxin I116 3.32x32 TM3 Van der Waals
C5a anaphylatoxin L117 3.33x33 TM3 hydrophobic
C5a anaphylatoxin L117 3.33x33 TM3 Van der Waals
C5a anaphylatoxin R175 ECL2 polar (charge-assisted hydrogen bond)
C5a anaphylatoxin Y181 ECL2 Van der Waals
C5a anaphylatoxin Y181 ECL2 polar (hydrogen bond)
C5a anaphylatoxin F182 ECL2 Van der Waals
C5a anaphylatoxin F182 ECL2 hydrophobic
C5a anaphylatoxin L187 ECL2 Van der Waals
C5a anaphylatoxin G189 45.51x51 ECL2 Van der Waals
C5a anaphylatoxin V190 45.52x52 ECL2 hydrophobic
C5a anaphylatoxin V190 45.52x52 ECL2 Van der Waals
C5a anaphylatoxin D191 ECL2 polar (charge-assisted hydrogen bond)
C5a anaphylatoxin Y192 ECL2 Van der Waals
C5a anaphylatoxin H194 ECL2 Van der Waals
C5a anaphylatoxin R206 5.42x43 TM5 Van der Waals
C5a anaphylatoxin Y258 6.51x51 TM6 polar (hydrogen bond)
C5a anaphylatoxin Y258 6.51x51 TM6 polar (hydrogen bond with backbone)
C5a anaphylatoxin Y258 6.51x51 TM6 Van der Waals
C5a anaphylatoxin G262 6.55x55 TM6 polar (hydrogen bond with backbone)
C5a anaphylatoxin G262 6.55x55 TM6 Van der Waals
C5a anaphylatoxin K279 7.32x31 TM7 Van der Waals
C5a anaphylatoxin K280 7.33x32 TM7 Van der Waals
C5a anaphylatoxin D282 7.35x34 TM7 polar (charge-assisted hydrogen bond)
C5a anaphylatoxin V286 7.39x38 TM7 Van der Waals

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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
2x63 2.63x63 S95
ECL1
23x50 23.50x50 W102
TM3
3x32 3.32x32 I116
3x33 3.33x33 L117
ECL2
45x51 45.51x51 G189
45x52 45.52x52 V190
TM5
5x43 5.42x43 R206
TM6
6x51 6.51x51 Y258
6x55 6.55x55 G262
TM7
7x31 7.32x31 K279
7x32 7.33x32 K280
7x34 7.35x34 D282
7x38 7.39x38 V286