PDB
8XQJ
Resolution
3.0 Å
Released
Jan. 22, 2025
Receptor
apelin
Class
A
Species
Homo sapiens
Ligand
Function
Single domain antibody JN241
Antagonist
Reference
10.1038/S41467-024-55555-6

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Ligand Amino Acid Generic Number Segment Interaction Type
Single domain antibody JN241 S17 N-term Van der Waals
Single domain antibody JN241 C19 N-term hydrophobic
Single domain antibody JN241 E20 N-term polar (hydrogen bond with backbone)
Single domain antibody JN241 Y21 N-term aromatic (edge-to-face)
Single domain antibody JN241 Y21 N-term polar (hydrogen bond)
Single domain antibody JN241 Y21 N-term hydrophobic
Single domain antibody JN241 T22 N-term Van der Waals
Single domain antibody JN241 D23 N-term polar (charge-charge)
Single domain antibody JN241 Y93 ECL1 aromatic (edge-to-face)
Single domain antibody JN241 F110 3.33x33 TM3 Van der Waals
Single domain antibody JN241 R168 4.64x65 TM4 polar (charge-charge)
Single domain antibody JN241 L173 ECL2 hydrophobic
Single domain antibody JN241 E174 ECL2 hydrophobic
Single domain antibody JN241 E174 ECL2 polar (hydrogen bond)
Single domain antibody JN241 T176 ECL2 polar (hydrogen bond)
Single domain antibody JN241 Q180 ECL2 Van der Waals
Single domain antibody JN241 Y182 45.51x51 ECL2 Van der Waals
Single domain antibody JN241 M183 45.52x52 ECL2 Van der Waals
Single domain antibody JN241 D184 ECL2 polar (charge-charge)
Single domain antibody JN241 Y185 ECL2 Van der Waals
Single domain antibody JN241 S186 ECL2 Van der Waals
Single domain antibody JN241 V191 ECL2 hydrophobic
Single domain antibody JN241 S192 ECL2 Van der Waals
Single domain antibody JN241 E194 5.31x32 TM5 polar (hydrogen bond)
Single domain antibody JN241 E194 5.31x32 TM5 polar (charge-charge)
Single domain antibody JN241 E198 5.35x36 TM5 Van der Waals
Single domain antibody JN241 Y264 6.51x51 TM6 Van der Waals
Single domain antibody JN241 V267 6.54x54 TM6 hydrophobic
Single domain antibody JN241 K268 6.55x55 TM6 polar (charge-charge)
Single domain antibody JN241 K268 6.55x55 TM6 polar (hydrogen bond)
Single domain antibody JN241 Y271 6.58x58 TM6 polar (hydrogen bond)
Single domain antibody JN241 Y271 6.58x58 TM6 hydrophobic
Single domain antibody JN241 C281 7.25x24 TM7 hydrophobic
Single domain antibody JN241 D284 7.28x27 TM7 hydrophobic
Single domain antibody JN241 L285 7.29x28 TM7 Van der Waals
Single domain antibody JN241 L287 7.31x30 TM7 Van der Waals
Single domain antibody JN241 M288 7.32x31 TM7 hydrophobic
Single domain antibody JN241 N289 7.33x32 TM7 Van der Waals
Single domain antibody JN241 F291 7.35x34 TM7 hydrophobic

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Snake plot — Download: PNG | SVG
ICL1 S R E K R ICL1ECL1 Y D W P F ECL1ICL2 P V A N A R L R ICL2ECL2 T T G D L E N T T K V Q C Y M D Y S M V A T V S ECL2ICL3 R K E ICL3ECL3 L H W ECL3N-term M E E G G D F D N Y Y G A D N Q S E C E Y T D W K S S G N-termC-term Q S R C A G T S H S S S G E K S A S Y S S G H S Q G P G P N M G K G G E Q M H E K S I P Y S Q E T L V V D C-term A L I P A I Y M L V F L L G T T G N G L V L W T V F R S R S A D I F I A S L A V A D L T F V V T L P L W A T Y T Y R D G T F F C K L S S Y L I F V N M Y A S V F C L T G L S F D R Y L A I V R L R V S G A V A T A V L W V L A A L L A M P V M V L R S E W A W E V G L G V S S T T V G F V V P F T I M L T C Y F F I A Q T I A G H F R I E G L R K R R R L L S I I V V L V V T F A L C W M P Y H L V K T L Y M L G S L P C D F D L F L M N I F P Y C T C I S Y V N S C L N P F L Y A F F D P R C T S G F R Q A M L C C
Helix box plot — Download: PNG | SVG G N G T T G L L F V L M Y I A P I L A 1 A S L A V A D L T F V V T L P L W A T Y 2 G T L C F V S A Y M N V F I L Y S S L K 3 G A V A T A V L W V L A A L L A M P V 4 Y C T L M I T F P V V F G V T T S S V G L 5 V V L V V T F A L C W M P Y H L V K T L 6 F P N L C S N V Y S I C T C Y P F I N 7

GPCRdb(A)
GPCRdb(A)
apelin receptor
TM3
3x33 3.33x33 F110
TM4
4x65 4.64x65 R168
ECL2
45x51 45.51x51 Y182
45x52 45.52x52 M183
TM5
5x32 5.31x32 E194
5x36 5.35x36 E198
TM6
6x51 6.51x51 Y264
6x54 6.54x54 V267
6x55 6.55x55 K268
6x58 6.58x58 Y271
TM7
7x24 7.25x24 C281
7x27 7.28x27 D284
7x28 7.29x28 L285
7x30 7.31x30 L287
7x31 7.32x31 M288
7x32 7.33x32 N289
7x34 7.35x34 F291