PDB
9KB9
Resolution
3.6 Å
Released
Oct. 15, 2025
Receptor
LGR4
Class
A
Species
Homo sapiens
Ligands
R-spondin-2
E3 ubiquitin-protein ligase ZNRF3
Function
Agonist
Agonist
Reference
10.1038/S41467-025-64129-Z
R-spondin-2 E3 ubiquitin-protein ligase ZNRF3

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Ligand Amino Acid Generic Number Segment Interaction Type
R-spondin-2 M66 N-term hydrophobic
R-spondin-2 A89 N-term hydrophobic
R-spondin-2 Q113 N-term polar (hydrogen bond)
R-spondin-2 Q113 N-term Van der Waals
R-spondin-2 N114 N-term polar (hydrogen bond)
R-spondin-2 D137 N-term polar (charge-assisted hydrogen bond)
R-spondin-2 A138 N-term Van der Waals
R-spondin-2 A138 N-term polar (hydrogen bond with backbone)
R-spondin-2 R156 N-term polar (charge-assisted hydrogen bond)
R-spondin-2 H157 N-term aromatic (face-to-edge)
R-spondin-2 H157 N-term Van der Waals
R-spondin-2 W159 N-term Van der Waals
R-spondin-2 W159 N-term aromatic (face-to-edge)
R-spondin-2 D161 N-term Van der Waals
R-spondin-2 D162 N-term polar (charge-assisted hydrogen bond)
R-spondin-2 Q180 N-term polar (hydrogen bond)
R-spondin-2 Q180 N-term Van der Waals
R-spondin-2 A181 N-term Van der Waals
R-spondin-2 A181 N-term hydrophobic
R-spondin-2 T183 N-term Van der Waals
R-spondin-2 L186 N-term Van der Waals
R-spondin-2 L186 N-term hydrophobic
R-spondin-2 V204 N-term hydrophobic
R-spondin-2 V204 N-term Van der Waals
R-spondin-2 V205 N-term hydrophobic
R-spondin-2 V205 N-term Van der Waals
R-spondin-2 H209 N-term Van der Waals
R-spondin-2 N210 N-term Van der Waals
R-spondin-2 E228 N-term polar (charge-assisted hydrogen bond)
R-spondin-2 T229 N-term polar (hydrogen bond)
R-spondin-2 E252 N-term polar (charge-assisted hydrogen bond)
E3 ubiquitin-protein ligase ZNRF3 R392 N-term polar (charge-assisted hydrogen bond)
E3 ubiquitin-protein ligase ZNRF3 G435 N-term Van der Waals
E3 ubiquitin-protein ligase ZNRF3 G435 N-term polar (hydrogen bond with backbone)
E3 ubiquitin-protein ligase ZNRF3 N437 N-term polar (hydrogen bond)
E3 ubiquitin-protein ligase ZNRF3 N437 N-term polar (hydrogen bond)
E3 ubiquitin-protein ligase ZNRF3 N437 N-term Van der Waals
E3 ubiquitin-protein ligase ZNRF3 N458 N-term Van der Waals
E3 ubiquitin-protein ligase ZNRF3 M540 1.34x34 TM1 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 M540 1.34x34 TM1 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 I541 1.35x35 TM1 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 I541 1.35x35 TM1 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 T544 1.38x38 TM1 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 F547 1.41x41 TM1 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 F547 1.41x41 TM1 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 E780 7.32x31 TM7 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 I781 7.33x32 TM7 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 I781 7.33x32 TM7 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 S784 7.36x35 TM7 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 F803 7.55x55 TM7 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 F803 7.55x55 TM7 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 K809 8.51x51 H8 Van der Waals

NGL is a WebGL based 3D viewer powered by MMTF.

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

GPCRdb(A)
GPCRdb(A)
LGR4
TM1
1x34 1.34x34 M540
1x35 1.35x35 I541
1x38 1.38x38 T544
1x41 1.41x41 F547
TM7
7x31 7.32x31 E780
7x32 7.33x32 I781
7x35 7.36x35 S784
7x55 7.55x55 F803
H8
8x51 8.51x51 K809