PDB
9EJC
Resolution
3.0 Å
Released
Sept. 3, 2025
Receptor
ORF74
Class
A
Species
Human herpesvirus 8 type P
Ligand
CXCL1
Function
Agonist
Reference
10.1038/S41467-025-63457-4

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Ligand Amino Acid Generic Number Segment Interaction Type
CXCL1 C30 N-term polar (hydrogen bond)
CXCL1 F32 N-term hydrophobic
CXCL1 F32 N-term Van der Waals
CXCL1 L34 N-term Van der Waals
CXCL1 L34 N-term polar (hydrogen bond with backbone)
CXCL1 E35 N-term polar (charge-assisted hydrogen bond)
CXCL1 V36 N-term Van der Waals
CXCL1 V36 N-term hydrophobic
CXCL1 S37 N-term polar (hydrogen bond with backbone)
CXCL1 S37 N-term Van der Waals
CXCL1 V38 N-term Van der Waals
CXCL1 E40 N-term Van der Waals
CXCL1 E103 2.60x60 TM2 polar (charge-assisted hydrogen bond)
CXCL1 E121 3.28x28 TM3 polar (charge-assisted hydrogen bond)
CXCL1 I122 3.29x29 TM3 hydrophobic
CXCL1 I122 3.29x29 TM3 Van der Waals
CXCL1 Y125 3.32x32 TM3 Van der Waals
CXCL1 Y125 3.32x32 TM3 hydrophobic
CXCL1 Y126 3.33x33 TM3 hydrophobic
CXCL1 Y126 3.33x33 TM3 Van der Waals
CXCL1 V186 ECL2 Van der Waals
CXCL1 V186 ECL2 hydrophobic
CXCL1 D188 ECL2 Van der Waals
CXCL1 P189 ECL2 Van der Waals
CXCL1 Y197 45.51x51 ECL2 Van der Waals
CXCL1 Y197 45.51x51 ECL2 hydrophobic
CXCL1 N199 ECL2 Van der Waals
CXCL1 R208 5.35x35 TM5 polar (charge-assisted hydrogen bond)
CXCL1 R212 5.39x39 TM5 polar (charge-assisted hydrogen bond)
CXCL1 D274 6.58x58 TM6 polar (charge-assisted hydrogen bond)
CXCL1 R278 6.62x62 TM6 polar (charge-assisted hydrogen bond)
CXCL1 D284 ECL3 Van der Waals
CXCL1 R289 7.28x27 TM7 polar (charge-assisted hydrogen bond)
CXCL1 N293 7.32x31 TM7 polar (hydrogen bond)
CXCL1 N293 7.32x31 TM7 Van der Waals
CXCL1 L296 7.35x34 TM7 Van der Waals
CXCL1 L296 7.35x34 TM7 hydrophobic

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Snake plot — Download: PNG | SVG
ECL1 P N I I ECL1ICL2 S T R S W P K ICL2ECL2 H R S R V V D P V S K Q A M C Y E N ECL2ICL3 K L Q ICL3ECL3 R W I R D ECL3N-term M A A E D F L T I F L D D D E S W N E T L N M S G Y D Y S G N F S L E V S V C E M T T V V N-termC-term T T C-term P Y T W N V G I L S L I F L I N V L G N G L V T Y I F C K H R S R A G A I D I L L L G I C L N S L C L S I S L L A E V L M F L F S T G L C R L E I F F Y Y L Y V Y L D I F S V V C V S L V R Y L L V A Y K Q S L G W V L T S A A L L I A L V L S G D A C R A G N M T A D W R L H V R T V S V T A G F L L P L A L L I L F Y A L T W C V V R R T A R R K V R G V I V A V V L L F F V F C F P Y H V L N L L D T L L R R S C Y T R G L I N V G L A V T S L L Q A L Y S A V V P L I Y S C L G S L F Y G L R Q S A R Q R M F Q S L F M S G
Helix box plot — Download: PNG | SVG G N G L V N I L F I L S L I G V N W T Y 1 L G I C L N S L C L S I S L L A E V L M 2 C V V S F I D L Y V Y L Y Y F F I E L R 3 G W V L T S A A L L I A L V L S G D A C 4 Y F L I L L A L P L L F G A T V S V T R 5 V A V V L L F F V F C F P Y H V L N L L 6 L P V V A S Y L A Q L L S T V A L G V 7

GPCRdb(A)
GPCRdb(A)
ORF74
TM2
2x60 2.60x60 E103
TM3
3x28 3.28x28 E121
3x29 3.29x29 I122
3x32 3.32x32 Y125
3x33 3.33x33 Y126
ECL2
45x51 45.51x51 Y197
TM5
5x35 5.35x35 R208
5x39 5.39x39 R212
TM6
6x58 6.58x58 D274
6x62 6.62x62 R278
TM7
7x27 7.28x27 R289
7x31 7.32x31 N293
7x34 7.35x34 L296