Structure information

C5a1 receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

6C1R

SPECIES

Homo sapiens

RESOLUTION

2.200

PREFERRED CHAIN

B

REFERENCE

10.1038/S41594-018-0067-Z

PUBLICATION DATE

May 30, 2018

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
PMX53 L178 2.60x60 TM2 hydrophobic
PMX53 I182 2.64x64 TM2 hydrophobic
PMX53 W188 23.50x50 ECL1 hydrophobic
PMX53 P199 3.29x29 TM3 polar (hydrogen bond with backbone)
PMX53 P199 3.29x29 TM3 Van der Waals
PMX53 I202 3.32x32 TM3 Van der Waals
avacopan I210 3.40x40 TM3 hydrophobic
avacopan L211 3.41x41 TM3 hydrophobic
avacopan A214 3.44x44 TM3 hydrophobic
avacopan A218 3.48x48 TM3 hydrophobic
avacopan F221 3.51x51 TM3 aromatic (face-to-edge)
avacopan A242 4.45x45 TM4 hydrophobic
avacopan V245 4.48x48 TM4 hydrophobic
avacopan A246 4.49x49 TM4 hydrophobic
PMX53 R261 4.64x65 TM4 polar (charge-assisted hydrogen bond)
PMX53 V262 ECL2 Van der Waals
PMX53 R264 ECL2 Van der Waals
PMX53 L273 ECL2 hydrophobic
PMX53 L273 ECL2 Van der Waals
PMX53 C274 45.50x50 ECL2 polar (hydrogen bond with backbone)
PMX53 C274 45.50x50 ECL2 Van der Waals
PMX53 G275 45.51x51 ECL2 Van der Waals
PMX53 V276 45.52x52 ECL2 polar (hydrogen bond with backbone)
PMX53 V276 45.52x52 ECL2 Van der Waals
PMX53 D277 ECL2 Van der Waals
PMX53 Y278 ECL2 Van der Waals
PMX53 Y278 ECL2 polar (hydrogen bond with backbone)
PMX53 S279 ECL2 Van der Waals
PMX53 E285 5.35x36 TM5 Van der Waals
PMX53 R292 5.42x43 TM5 polar (charge-assisted hydrogen bond)
avacopan W299 5.49x49 TM5 Van der Waals
avacopan W299 5.49x49 TM5 polar (hydrogen bond)
avacopan W299 5.49x49 TM5 aromatic (edge-to-face)
avacopan P300 5.50x50 TM5 Van der Waals
avacopan P300 5.50x50 TM5 hydrophobic
avacopan T303 5.53x53 TM5 Van der Waals
avacopan T303 5.53x53 TM5 polar (hydrogen bond with backbone)
avacopan L304 5.54x54 TM5 Van der Waals
avacopan C307 5.57x57 TM5 hydrophobic
avacopan C307 5.57x57 TM5 Van der Waals
PMX53 Y344 6.51x51 TM6 polar (hydrogen bond)
PMX53 Y344 6.51x51 TM6 polar (hydrogen bond with backbone)
PMX53 T347 6.54x54 TM6 polar (hydrogen bond)
PMX53 G348 6.55x55 TM6 Van der Waals
PMX53 M351 6.58x58 TM6 Van der Waals
PMX53 M351 6.58x58 TM6 hydrophobic
PMX53 K365 7.32x31 TM7 Van der Waals
PMX53 D368 7.35x34 TM7 polar (charge-assisted hydrogen bond)
PMX53 S369 7.36x35 TM7 Van der Waals
PMX53 V372 7.39x38 TM7 Van der Waals
PMX53 V372 7.39x38 TM7 hydrophobic

Ligands

PMX53

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avacopan

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Residue Diagrams

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
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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
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Residue Table


GPCRdb(A)
GPCRdb(A)
C5a1 receptor
TM2
2x60 2.60x60 L92
2x64 2.64x64 I96
ECL1
23x50 23.50x50 W102
TM3
3x29 3.29x29 P113
3x32 3.32x32 I116
3x40 3.40x40 I124
3x41 3.41x41 L125
3x44 3.44x44 A128
3x48 3.48x48 A132
3x51 3.51x51 F135
TM4
4x45 4.45x45 A156
4x48 4.48x48 V159
4x49 4.49x49 A160
4x65 4.64x65 R175
ECL2
45x50 45.50x50 C188
45x51 45.51x51 G189
45x52 45.52x52 V190
TM5
5x36 5.35x36 E199
5x43 5.42x43 R206
5x49 5.49x49 W213
5x50 5.50x50 P214
5x53 5.53x53 T217
5x54 5.54x54 L218
5x57 5.57x57 C221
TM6
6x51 6.51x51 Y258
6x54 6.54x54 T261
6x55 6.55x55 G262
6x58 6.58x58 M265
TM7
7x31 7.32x31 K279
7x34 7.35x34 D282
7x35 7.36x35 S283
7x38 7.39x38 V286