PDB
7SK5
Resolution
4.0 Å
Released
July 27, 2022
Receptor
ACKR3
Class
A
Species
Homo sapiens
Ligand
CXCL12
Function
Agonist
Reference
10.1126/SCIADV.ABN8063

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Ligand Amino Acid Generic Number Segment Interaction Type
CXCL12 V28 N-term polar (hydrogen bond with backbone)
CXCL12 V28 N-term polar (hydrogen bond)
CXCL12 V29 N-term polar (hydrogen bond)
CXCL12 V29 N-term polar (hydrogen bond with backbone)
CXCL12 D30 N-term polar (hydrogen bond with backbone)
CXCL12 D30 N-term polar (charge-assisted hydrogen bond)
CXCL12 T31 N-term polar (hydrogen bond)
CXCL12 V32 N-term polar (hydrogen bond with backbone)
CXCL12 V32 N-term polar (hydrogen bond)
CXCL12 M33 N-term polar (hydrogen bond)
CXCL12 C34 N-term polar (hydrogen bond)
CXCL12 W100 2.60x60 TM2 Van der Waals
CXCL12 W100 2.60x60 TM2 hydrophobic
CXCL12 S103 2.63x63 TM2 polar (hydrogen bond)
CXCL12 L104 2.64x64 TM2 Van der Waals
CXCL12 N108 ECL1 polar (hydrogen bond)
CXCL12 W110 23.50x50 ECL1 Van der Waals
CXCL12 C117 3.25x25 TM3 polar (hydrogen bond)
CXCL12 H121 3.29x29 TM3 polar (hydrogen bond)
CXCL12 F124 3.32x32 TM3 Van der Waals
CXCL12 D179 4.60x61 TM4 polar (charge-assisted hydrogen bond)
CXCL12 L183 ECL2 Van der Waals
CXCL12 C196 45.50x50 ECL2 Van der Waals
CXCL12 C196 45.50x50 ECL2 polar (hydrogen bond with backbone)
CXCL12 R197 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
CXCL12 S198 45.52x52 ECL2 polar (hydrogen bond)
CXCL12 Y200 ECL2 Van der Waals
CXCL12 I205 5.31x32 TM5 Van der Waals
CXCL12 I205 5.31x32 TM5 hydrophobic
CXCL12 K206 5.32x33 TM5 polar (charge-assisted hydrogen bond)
CXCL12 E213 5.39x40 TM5 Van der Waals
CXCL12 Y268 6.51x51 TM6 polar (hydrogen bond)
CXCL12 Y268 6.51x51 TM6 polar (charge-assisted hydrogen bond)
CXCL12 Y268 6.51x51 TM6 polar (hydrogen bond)
CXCL12 D275 6.58x58 TM6 polar (charge-assisted hydrogen bond)
CXCL12 D275 6.58x58 TM6 polar (charge-charge)
CXCL12 I279 6.62x62 TM6 polar (charge-assisted hydrogen bond)
CXCL12 L280 6.63x63 TM6 Van der Waals
CXCL12 H281 6.64x64 TM6 polar (hydrogen bond)
CXCL12 Y282 ECL3 polar (charge-assisted hydrogen bond)
CXCL12 F285 ECL3 hydrophobic
CXCL12 F285 ECL3 Van der Waals
CXCL12 L297 7.35x34 TM7 polar (charge-assisted hydrogen bond)
CXCL12 H298 7.36x35 TM7 polar (hydrogen bond)
CXCL12 Q301 7.39x38 TM7 polar (hydrogen bond)
CXCL12 Q301 7.39x38 TM7 polar (hydrogen bond)

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Snake plot — Download: PNG | SVG
ICL1 K T T G ICL1ECL1 H N Q W P M ECL1ICL2 F T N T P S S R K K M ICL2ECL2 K T V T S A S N N E T Y C R S F Y P E H ECL2ICL3 S D ICL3ECL3 Y I P F ECL3N-term M D L H L F D Y S E P G N F S D I S W P C N S S D C I V V D T V M C P N M P N K N-termC-term Y S A K T G L T K L I D A S R V S E T E Y S A L E Q S T K C-term S V L L Y T L S F I Y I F I F V I G M I A N S V V V W V N I Q A Y D T H C Y I L N L A I A D L W V V L T I P V W V V S L V Q G E L T C K V T H L I F S I N L F G S I F F L T C M S V D R Y L S I T Y V R R V V C I L V W L L A F C V S L P D T Y Y L S I K E W L I G M E L V S V V L G F A V P F S I I A V F Y F L L A R A I S A S Q E K H S S R K I I F S Y V V V F L V C W L P Y H V A V L L D I F S I L H T C R L E H A L F T A L H V T Q C L S L V H C C V N P V L Y S F I N R N L M K K Y R Y E A F I F
Helix box plot — Download: PNG | SVG S N A I M G I V F I F I Y I F S L T Y L 1 L N L A I A D L W V V L T I P V W V V S 2 C T L F F I S G F L N I S F I L H T V K 3 R R V V C I L V W L L A F C V S L P D 4 Y F V A I I S F P V A F G L V V S V L E M 5 F S Y V V V F L V C W L P Y H V A V L L 6 V P N V C C H V L S L C Q T V H L A T 7

GPCRdb(A)
GPCRdb(A)
ACKR3
TM2
2x60 2.60x60 W100
2x63 2.63x63 S103
2x64 2.64x64 L104
ECL1
23x50 23.50x50 W110
TM3
3x25 3.25x25 C117
3x29 3.29x29 H121
3x32 3.32x32 F124
TM4
4x61 4.60x61 D179
ECL2
45x50 45.50x50 C196
45x51 45.51x51 R197
45x52 45.52x52 S198
TM5
5x32 5.31x32 I205
5x33 5.32x33 K206
5x40 5.39x40 E213
TM6
6x51 6.51x51 Y268
6x58 6.58x58 D275
6x62 6.62x62 I279
6x63 6.63x63 L280
6x64 6.64x64 H281
TM7
7x34 7.35x34 L297
7x35 7.36x35 H298
7x38 7.39x38 Q301