PDB
8HK5
Resolution
3.0 Å
Released
May 10, 2023
Receptor
C5a1
Class
A
Species
Homo sapiens
Ligand
[125I]C5a (human)
Function
Agonist
Reference
10.1038/S41589-023-01339-W

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Ligand Amino Acid Generic Number Segment Interaction Type
[125I]C5a (human) L22 N-term polar (hydrogen bond with backbone)
[125I]C5a (human) L22 N-term Van der Waals
[125I]C5a (human) P25 N-term Van der Waals
[125I]C5a (human) V26 N-term Van der Waals
[125I]C5a (human) V26 N-term polar (hydrogen bond with backbone)
[125I]C5a (human) D27 N-term Van der Waals
[125I]C5a (human) D27 N-term polar (hydrogen bond with backbone)
[125I]C5a (human) K28 N-term Van der Waals
[125I]C5a (human) T29 N-term Van der Waals
[125I]C5a (human) R34 1.29x29 TM1 Van der Waals
[125I]C5a (human) I91 2.59x59 TM2 hydrophobic
[125I]C5a (human) I91 2.59x59 TM2 Van der Waals
[125I]C5a (human) L92 2.60x60 TM2 hydrophobic
[125I]C5a (human) L92 2.60x60 TM2 Van der Waals
[125I]C5a (human) H100 ECL1 Van der Waals
[125I]C5a (human) P113 3.29x29 TM3 hydrophobic
[125I]C5a (human) P113 3.29x29 TM3 Van der Waals
[125I]C5a (human) I116 3.32x32 TM3 hydrophobic
[125I]C5a (human) I116 3.32x32 TM3 Van der Waals
[125I]C5a (human) L117 3.33x33 TM3 Van der Waals
[125I]C5a (human) L117 3.33x33 TM3 hydrophobic
[125I]C5a (human) M120 3.36x36 TM3 Van der Waals
[125I]C5a (human) R175 ECL2 polar (charge-assisted hydrogen bond)
[125I]C5a (human) V176 ECL2 polar (hydrogen bond with backbone)
[125I]C5a (human) V176 ECL2 Van der Waals
[125I]C5a (human) R178 ECL2 Van der Waals
[125I]C5a (human) Y181 ECL2 hydrophobic
[125I]C5a (human) Y181 ECL2 Van der Waals
[125I]C5a (human) F182 ECL2 hydrophobic
[125I]C5a (human) F182 ECL2 Van der Waals
[125I]C5a (human) C188 45.50x50 ECL2 Van der Waals
[125I]C5a (human) G189 45.51x51 ECL2 polar (hydrogen bond with backbone)
[125I]C5a (human) G189 45.51x51 ECL2 Van der Waals
[125I]C5a (human) V190 45.52x52 ECL2 Van der Waals
[125I]C5a (human) V190 45.52x52 ECL2 polar (hydrogen bond with backbone)
[125I]C5a (human) D191 ECL2 polar (charge-assisted hydrogen bond)
[125I]C5a (human) S193 ECL2 Van der Waals
[125I]C5a (human) H194 ECL2 Van der Waals
[125I]C5a (human) H194 ECL2 polar (hydrogen bond)
[125I]C5a (human) H194 ECL2 polar (hydrogen bond with backbone)
[125I]C5a (human) E199 5.35x36 TM5 polar (charge-assisted hydrogen bond)
[125I]C5a (human) R206 5.42x43 TM5 Van der Waals
[125I]C5a (human) Y258 6.51x51 TM6 Van der Waals
[125I]C5a (human) Y258 6.51x51 TM6 polar (hydrogen bond with backbone)
[125I]C5a (human) T261 6.54x54 TM6 polar (hydrogen bond)
[125I]C5a (human) T261 6.54x54 TM6 Van der Waals
[125I]C5a (human) G262 6.55x55 TM6 Van der Waals
[125I]C5a (human) G262 6.55x55 TM6 polar (hydrogen bond with backbone)
[125I]C5a (human) F275 7.28x27 TM7 Van der Waals
[125I]C5a (human) F275 7.28x27 TM7 hydrophobic
[125I]C5a (human) L276 7.29x28 TM7 hydrophobic
[125I]C5a (human) L276 7.29x28 TM7 Van der Waals
[125I]C5a (human) K279 7.32x31 TM7 Van der Waals
[125I]C5a (human) K280 7.33x32 TM7 Van der Waals
[125I]C5a (human) D282 7.35x34 TM7 polar (charge-assisted hydrogen bond)
[125I]C5a (human) S283 7.36x35 TM7 polar (hydrogen bond with backbone)
[125I]C5a (human) S283 7.36x35 TM7 polar (hydrogen bond)
[125I]C5a (human) S283 7.36x35 TM7 polar (hydrogen bond)
[125I]C5a (human) S283 7.36x35 TM7 Van der Waals

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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
TM1
1x29 1.29x29 R34
TM2
2x59 2.59x59 I91
2x60 2.60x60 L92
TM3
3x29 3.29x29 P113
3x32 3.32x32 I116
3x33 3.33x33 L117
3x36 3.36x36 M120
ECL2
45x50 45.50x50 C188
45x51 45.51x51 G189
45x52 45.52x52 V190
TM5
5x36 5.35x36 E199
5x43 5.42x43 R206
TM6
6x51 6.51x51 Y258
6x54 6.54x54 T261
6x55 6.55x55 G262
TM7
7x27 7.28x27 F275
7x28 7.29x28 L276
7x31 7.32x31 K279
7x32 7.33x32 K280
7x34 7.35x34 D282
7x35 7.36x35 S283