PDB
Resolution
3.0 Å
Released
Sept. 3, 2025
Receptor
Class
A
Species
Human herpesvirus 8 type P
Ligand
Function
CXCL1
Agonist

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Ligand Amino Acid Generic Number Segment Interaction Type
CXCL1 C30 N-term covalent bond
CXCL1 N31 N-term Van der Waals
CXCL1 F32 N-term hydrophobic
CXCL1 L34 N-term polar (hydrogen bond with backbone)
CXCL1 E35 N-term polar (hydrogen bond)
CXCL1 E35 N-term polar (charge-charge)
CXCL1 V36 N-term hydrophobic
CXCL1 S37 N-term Van der Waals
CXCL1 V38 N-term hydrophobic
CXCL1 C39 N-term Van der Waals
CXCL1 E40 N-term polar (charge-charge)
CXCL1 L54 1.39x39 TM1 hydrophobic
CXCL1 E103 2.60x60 TM2 polar (charge-charge)
CXCL1 E103 2.60x60 TM2 polar (hydrogen bond)
CXCL1 E121 3.28x28 TM3 polar (hydrogen bond)
CXCL1 E121 3.28x28 TM3 polar (charge-charge)
CXCL1 I122 3.29x29 TM3 hydrophobic
CXCL1 Y125 3.32x32 TM3 hydrophobic
CXCL1 Y126 3.33x33 TM3 Van der Waals
CXCL1 V186 ECL2 hydrophobic
CXCL1 D188 ECL2 Van der Waals
CXCL1 P189 ECL2 Van der Waals
CXCL1 Y197 45.51x51 ECL2 hydrophobic
CXCL1 E198 45.52x52 ECL2 Van der Waals
CXCL1 N199 ECL2 Van der Waals
CXCL1 T204 5.31x31 TM5 Van der Waals
CXCL1 R208 5.35x35 TM5 polar (charge-charge)
CXCL1 R208 5.35x35 TM5 polar (hydrogen bond)
CXCL1 R212 5.39x39 TM5 polar (charge-charge)
CXCL1 R212 5.39x39 TM5 polar (hydrogen bond)
CXCL1 Y267 6.51x51 TM6 Van der Waals
CXCL1 D274 6.58x58 TM6 polar (hydrogen bond)
CXCL1 D274 6.58x58 TM6 polar (charge-charge)
CXCL1 L277 6.61x61 TM6 Van der Waals
CXCL1 R278 6.62x62 TM6 polar (charge-charge)
CXCL1 R278 6.62x62 TM6 polar (hydrogen bond)
CXCL1 D284 ECL3 Van der Waals
CXCL1 R289 7.28x27 TM7 polar (hydrogen bond)
CXCL1 I292 7.31x30 TM7 Van der Waals
CXCL1 N293 7.32x31 TM7 polar (hydrogen bond)
CXCL1 L296 7.35x34 TM7 hydrophobic
CXCL1 A297 7.36x35 TM7 Van der Waals
CXCL1 S300 7.39x38 TM7 Van der Waals

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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
TM1
1x39 1.39x39 L54
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
45x52 45.52x52 E198
TM5
5x31 5.31x31 T204
5x35 5.35x35 R208
5x39 5.39x39 R212
TM6
6x51 6.51x51 Y267
6x58 6.58x58 D274
6x61 6.61x61 L277
6x62 6.62x62 R278
TM7
7x27 7.28x27 R289
7x30 7.31x30 I292
7x31 7.32x31 N293
7x34 7.35x34 L296
7x35 7.36x35 A297
7x38 7.39x38 S300