PDB
9KB8
Resolution
3.3 Å
Released
Oct. 15, 2025
Receptor
LGR4
Class
A
Species
Homo sapiens
Ligands
R-spondin-2
ZNRF3
Function
Agonist
Unknown
Reference
10.1038/S41467-025-64129-Z
R-spondin-2 ZNRF3

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Ligand Amino Acid Generic Number Segment Interaction Type
R-spondin-2 M66 N-term polar (hydrogen bond)
R-spondin-2 G90 N-term Van der Waals
R-spondin-2 Q113 N-term Van der Waals
R-spondin-2 Q113 N-term polar (hydrogen bond)
R-spondin-2 N114 N-term polar (hydrogen bond)
R-spondin-2 N114 N-term Van der Waals
R-spondin-2 D137 N-term polar (charge-assisted hydrogen bond)
R-spondin-2 A138 N-term hydrophobic
R-spondin-2 A138 N-term Van der Waals
R-spondin-2 H140 N-term Van der Waals
R-spondin-2 R156 N-term Van der Waals
R-spondin-2 H157 N-term Van der Waals
R-spondin-2 H157 N-term aromatic (face-to-edge)
R-spondin-2 W159 N-term Van der Waals
R-spondin-2 W159 N-term hydrophobic
R-spondin-2 D161 N-term Van der Waals
R-spondin-2 D162 N-term Van der Waals
R-spondin-2 Q180 N-term polar (hydrogen bond)
R-spondin-2 A181 N-term Van der Waals
R-spondin-2 A181 N-term hydrophobic
R-spondin-2 L182 N-term Van der Waals
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 Van der Waals
R-spondin-2 V205 N-term hydrophobic
R-spondin-2 H207 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 T229 N-term Van der Waals
R-spondin-2 T229 N-term polar (hydrogen bond)
R-spondin-2 E252 N-term polar (charge-assisted hydrogen bond)
ZNRF3 G435 N-term polar (hydrogen bond with backbone)
ZNRF3 G435 N-term Van der Waals
ZNRF3 N437 N-term Van der Waals
ZNRF3 N437 N-term polar (hydrogen bond)
ZNRF3 N458 N-term Van der Waals
ZNRF3 R460 N-term polar (charge-assisted hydrogen bond)
ZNRF3 C476 N-term polar (hydrogen bond)
ZNRF3 M540 1.34x34 TM1 hydrophobic
ZNRF3 M540 1.34x34 TM1 Van der Waals
ZNRF3 I541 1.35x35 TM1 hydrophobic
ZNRF3 I541 1.35x35 TM1 Van der Waals
ZNRF3 S778 7.30x29 TM7 Van der Waals
ZNRF3 E780 7.32x31 TM7 Van der Waals
ZNRF3 I781 7.33x32 TM7 hydrophobic
ZNRF3 I781 7.33x32 TM7 Van der Waals
ZNRF3 I788 7.40x39 TM7 hydrophobic

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

Download PDB file

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

Download PDB file

Snake plot — Download: PNG | SVG
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
TM7
7x29 7.30x29 S778
7x31 7.32x31 E780
7x32 7.33x32 I781
7x39 7.40x39 I788