PDB
8XFT
Resolution
3.2 Å
Released
Dec. 4, 2024
Receptor
LGR4
Class
A
Species
Homo sapiens
Ligands
R-spondin-2
E3 ubiquitin-protein ligase ZNRF3
Function
Agonist
Unknown
Reference
—
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 Q113 N-term polar (hydrogen bond)
R-spondin-2 Q113 N-term Van der Waals
R-spondin-2 N114 N-term Van der Waals
R-spondin-2 N114 N-term polar (hydrogen bond)
R-spondin-2 D137 N-term Van der Waals
R-spondin-2 A138 N-term Van der Waals
R-spondin-2 A138 N-term polar (hydrogen bond with backbone)
R-spondin-2 H140 N-term Van der Waals
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 hydrophobic
R-spondin-2 W159 N-term Van der Waals
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 Q180 N-term Van der Waals
R-spondin-2 A181 N-term hydrophobic
R-spondin-2 A181 N-term Van der Waals
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 N210 N-term Van der Waals
R-spondin-2 N226 N-term polar (hydrogen bond)
R-spondin-2 E252 N-term polar (charge-assisted hydrogen bond)
E3 ubiquitin-protein ligase ZNRF3 S538 1.32x32 TM1 polar (hydrogen bond)
E3 ubiquitin-protein ligase ZNRF3 M540 1.34x34 TM1 polar (hydrogen bond)
E3 ubiquitin-protein ligase ZNRF3 I541 1.35x35 TM1 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 I541 1.35x35 TM1 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 T544 1.38x38 TM1 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 F547 1.41x41 TM1 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 F547 1.41x41 TM1 aromatic (face-to-edge)
E3 ubiquitin-protein ligase ZNRF3 I548 1.42x42 TM1 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 I548 1.42x42 TM1 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 I781 7.33x32 TM7 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 I781 7.33x32 TM7 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 S784 7.36x35 TM7 polar (hydrogen bond)
E3 ubiquitin-protein ligase ZNRF3 S784 7.36x35 TM7 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 I788 7.40x39 TM7 hydrophobic
E3 ubiquitin-protein ligase ZNRF3 I788 7.40x39 TM7 Van der Waals
E3 ubiquitin-protein ligase ZNRF3 L792 7.44x43 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

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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
1x32 1.32x32 S538
1x34 1.34x34 M540
1x35 1.35x35 I541
1x38 1.38x38 T544
1x41 1.41x41 F547
1x42 1.42x42 I548
TM7
7x32 7.33x32 I781
7x35 7.36x35 S784
7x39 7.40x39 I788
7x43 7.44x43 L792
7x55 7.55x55 F803