Structure information

LGR4

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

9KB8

SPECIES

Homo sapiens

RESOLUTION

3.250

PREFERRED CHAIN

A

REFERENCE

10.1038/S41467-025-64129-Z

PUBLICATION DATE

Oct. 15, 2025

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
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

Ligands

R-spondin-2

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ZNRF3

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Residue Diagrams

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
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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
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Residue Table


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