PDB
7X9B
Resolution
3.4 Å
Released
May 18, 2022
Receptor
Y2
Class
A
Species
Homo sapiens
Ligand
Function
NEUROPEPTIDE-Y
Agonist
Reference
10.1126/SCIADV.ABM1232

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Ligand Amino Acid Generic Number Segment Interaction Type
NEUROPEPTIDE-Y L40 N-term Van der Waals
NEUROPEPTIDE-Y T107 2.61x60 TM2 polar (hydrogen bond)
NEUROPEPTIDE-Y Y110 2.64x63 TM2 hydrophobic
NEUROPEPTIDE-Y T111 2.65x64 TM2 Van der Waals
NEUROPEPTIDE-Y Q130 3.32x32 TM3 Van der Waals
NEUROPEPTIDE-Y L183 4.60x61 TM4 hydrophobic
NEUROPEPTIDE-Y I192 ECL2 Van der Waals
NEUROPEPTIDE-Y I194 ECL2 hydrophobic
NEUROPEPTIDE-Y I195 ECL2 hydrophobic
NEUROPEPTIDE-Y F198 ECL2 Van der Waals
NEUROPEPTIDE-Y I200 ECL2 Van der Waals
NEUROPEPTIDE-Y A202 ECL2 hydrophobic
NEUROPEPTIDE-Y T204 45.51x51 ECL2 Van der Waals
NEUROPEPTIDE-Y E205 45.52x52 ECL2 polar (charge-charge)
NEUROPEPTIDE-Y E210 ECL2 Van der Waals
NEUROPEPTIDE-Y E211 ECL2 hydrophobic
NEUROPEPTIDE-Y Y219 5.38x39 TM5 Van der Waals
NEUROPEPTIDE-Y S220 5.39x40 TM5 Van der Waals
NEUROPEPTIDE-Y L227 5.46x461 TM5 Van der Waals
NEUROPEPTIDE-Y H285 6.52x52 TM6 Van der Waals
NEUROPEPTIDE-Y Q288 6.55x55 TM6 polar (hydrogen bond)
NEUROPEPTIDE-Y V291 6.58x58 TM6 Van der Waals
NEUROPEPTIDE-Y D292 6.59x59 TM6 polar (charge-charge)
NEUROPEPTIDE-Y Q296 ECL3 Van der Waals
NEUROPEPTIDE-Y L298 ECL3 hydrophobic
NEUROPEPTIDE-Y D299 ECL3 polar (hydrogen bond)
NEUROPEPTIDE-Y D299 ECL3 polar (charge-charge)
NEUROPEPTIDE-Y L300 ECL3 Van der Waals
NEUROPEPTIDE-Y K301 ECL3 Van der Waals
NEUROPEPTIDE-Y Y303 7.31x30 TM7 hydrophobic
NEUROPEPTIDE-Y F307 7.35x34 TM7 Van der Waals
NEUROPEPTIDE-Y H311 7.39x38 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
Y2 receptor
TM2
2x60 2.61x60 T107
2x63 2.64x63 Y110
2x64 2.65x64 T111
TM3
3x32 3.32x32 Q130
TM4
4x61 4.60x61 L183
ECL2
45x51 45.51x51 T204
45x52 45.52x52 E205
TM5
5x39 5.38x39 Y219
5x40 5.39x40 S220
5x461 5.46x461 L227
TM6
6x52 6.52x52 H285
6x55 6.55x55 Q288
6x58 6.58x58 V291
6x59 6.59x59 D292
TM7
7x30 7.31x30 Y303
7x34 7.35x34 F307
7x38 7.39x38 H311