PDB
7Y1F
Resolution
3.3 Å
Released
May 24, 2023
Receptor
κ
Class
A
Species
Homo sapiens
Ligand
Dynorphin A13
Function
Agonist
Reference
10.1093/PROCEL/PWAC033

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Ligand Amino Acid Generic Number Segment Interaction Type
Dynorphin A13 Q217 2.60x60 TM2 Van der Waals
Dynorphin A13 Q217 2.60x60 TM2 polar (hydrogen bond)
Dynorphin A13 N224 2.67x67 TM2 polar (hydrogen bond)
Dynorphin A13 N224 2.67x67 TM2 polar (hydrogen bond)
Dynorphin A13 L237 3.29x29 TM3 Van der Waals
Dynorphin A13 L237 3.29x29 TM3 hydrophobic
Dynorphin A13 D240 3.32x32 TM3 Van der Waals
Dynorphin A13 Y241 3.33x33 TM3 polar (hydrogen bond)
Dynorphin A13 Y241 3.33x33 TM3 polar (hydrogen bond)
Dynorphin A13 Y241 3.33x33 TM3 Van der Waals
Dynorphin A13 M244 3.36x36 TM3 Van der Waals
Dynorphin A13 M244 3.36x36 TM3 hydrophobic
Dynorphin A13 C312 45.50x50 ECL2 Van der Waals
Dynorphin A13 S313 45.51x51 ECL2 Van der Waals
Dynorphin A13 L314 45.52x52 ECL2 Van der Waals
Dynorphin A13 Q315 ECL2 Van der Waals
Dynorphin A13 F316 ECL2 Van der Waals
Dynorphin A13 F316 ECL2 polar (hydrogen bond with backbone)
Dynorphin A13 Y321 ECL2 hydrophobic
Dynorphin A13 Y321 ECL2 Van der Waals
Dynorphin A13 D325 5.35x36 TM5 polar (charge-assisted hydrogen bond)
Dynorphin A13 K329 5.39x40 TM5 Van der Waals
Dynorphin A13 V332 5.42x43 TM5 hydrophobic
Dynorphin A13 V332 5.42x43 TM5 Van der Waals
Dynorphin A13 W389 6.48x48 TM6 hydrophobic
Dynorphin A13 I396 6.55x55 TM6 hydrophobic
Dynorphin A13 I396 6.55x55 TM6 Van der Waals
Dynorphin A13 H406 ECL3 Van der Waals
Dynorphin A13 H406 ECL3 polar (hydrogen bond)
Dynorphin A13 L411 7.32x31 TM7 Van der Waals
Dynorphin A13 L411 7.32x31 TM7 hydrophobic
Dynorphin A13 Y414 7.35x34 TM7 polar (hydrogen bond)
Dynorphin A13 Y414 7.35x34 TM7 polar (hydrogen bond)
Dynorphin A13 I418 7.39x38 TM7 hydrophobic
Dynorphin A13 I418 7.39x38 TM7 Van der Waals
Dynorphin A13 Y422 7.43x42 TM7 polar (hydrogen bond)
Dynorphin A13 Y422 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
κ receptor
TM2
2x60 2.60x60 Q115
2x67 2.67x67 N122
TM3
3x29 3.29x29 I135
3x32 3.32x32 D138
3x33 3.33x33 Y139
3x36 3.36x36 M142
ECL2
45x50 45.50x50 C210
45x51 45.51x51 S211
45x52 45.52x52 L212
TM5
5x36 5.35x36 D223
5x40 5.39x40 K227
5x43 5.42x43 V230
TM6
6x48 6.48x48 W287
6x55 6.55x55 I294
TM7
7x31 7.32x31 L309
7x34 7.35x34 Y312
7x38 7.39x38 I316
7x42 7.43x42 Y320