PDB
7SK7
Resolution
3.3 Å
Released
July 27, 2022
Receptor
ACKR3
Class
A
Species
Homo sapiens
Ligands
CXCL12
CCX662
Function
Agonist
Agonist (partial)
Reference
10.1126/SCIADV.ABN8063
CXCL12 CCX662

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Ligand Amino Acid Generic Number Segment Interaction Type
CXCL12 C26 N-term polar (hydrogen bond)
CXCL12 I27 N-term polar (hydrogen bond with backbone)
CXCL12 I27 N-term polar (hydrogen bond)
CXCL12 V28 N-term polar (hydrogen bond with backbone)
CXCL12 V28 N-term polar (hydrogen bond)
CXCL12 V29 N-term polar (hydrogen bond)
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)
CXCL12 V32 N-term polar (hydrogen bond with backbone)
CXCL12 M33 N-term polar (hydrogen bond)
CXCL12 C34 N-term polar (hydrogen bond)
CXCL12 C34 N-term polar (hydrogen bond with backbone)
CXCL12 N36 N-term polar (hydrogen bond)
CCX662 Y51 1.39x39 TM1 polar (hydrogen bond)
CCX662 W100 2.60x60 TM2 polar (hydrogen bond)
CCX662 S103 2.63x63 TM2 polar (hydrogen bond)
CCX662 S103 2.63x63 TM2 polar (hydrogen bond)
CCX662 L104 2.64x64 TM2 Van der Waals
CCX662 N108 ECL1 polar (hydrogen bond)
CCX662 H121 3.29x29 TM3 polar (hydrogen bond)
CCX662 F124 3.32x32 TM3 polar (hydrogen bond)
CCX662 S125 3.33x33 TM3 polar (hydrogen bond)
CCX662 L128 3.36x36 TM3 polar (hydrogen bond)
CCX662 F129 3.37x37 TM3 hydrophobic
CCX662 F129 3.37x37 TM3 Van der Waals
CCX662 I132 3.40x40 TM3 polar (hydrogen bond)
CXCL12 S190 ECL2 Van der Waals
CXCL12 N191 ECL2 polar (hydrogen bond)
CXCL12 N191 ECL2 polar (hydrogen bond)
CXCL12 Y195 ECL2 Van der Waals
CXCL12 Y195 ECL2 hydrophobic
CXCL12 R197 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
CXCL12 E202 ECL2 polar (charge-assisted hydrogen bond)
CXCL12 I205 5.31x32 TM5 polar (hydrogen bond)
CXCL12 K206 5.32x33 TM5 Van der Waals
CXCL12 L209 5.35x36 TM5 Van der Waals
CXCL12 L209 5.35x36 TM5 hydrophobic
CCX662 S216 5.42x43 TM5 Van der Waals
CCX662 G220 5.46x461 TM5 polar (hydrogen bond)
CCX662 G220 5.46x461 TM5 polar (hydrogen bond with backbone)
CCX662 W265 6.48x48 TM6 hydrophobic
CCX662 W265 6.48x48 TM6 Van der Waals
CCX662 Y268 6.51x51 TM6 polar (hydrogen bond)
CCX662 Y268 6.51x51 TM6 aromatic (face-to-edge)
CCX662 H269 6.52x52 TM6 polar (hydrogen bond)
CXCL12 D275 6.58x58 TM6 polar (charge-assisted hydrogen bond)
CXCL12 I279 6.62x62 TM6 polar (hydrogen bond)
CXCL12 I279 6.62x62 TM6 polar (charge-assisted hydrogen bond)
CXCL12 L280 6.63x63 TM6 polar (hydrogen bond with backbone)
CXCL12 L280 6.63x63 TM6 polar (charge-assisted hydrogen bond)
CXCL12 H281 6.64x64 TM6 polar (hydrogen bond with backbone)
CXCL12 H281 6.64x64 TM6 polar (hydrogen bond)
CXCL12 Y282 ECL3 Van der Waals
CXCL12 F285 ECL3 hydrophobic
CXCL12 F285 ECL3 Van der Waals
CXCL12 E290 7.28x27 TM7 polar (charge-assisted hydrogen bond)
CXCL12 E290 7.28x27 TM7 polar (charge-charge)
CXCL12 E290 7.28x27 TM7 polar (hydrogen bond with backbone)
CXCL12 L293 7.31x30 TM7 Van der Waals
CXCL12 F294 7.32x31 TM7 polar (charge-assisted hydrogen bond)
CXCL12 F294 7.32x31 TM7 polar (hydrogen bond)
CXCL12 F294 7.32x31 TM7 polar (hydrogen bond with backbone)
CXCL12 L297 7.35x34 TM7 polar (hydrogen bond)
CCX662 Q301 7.39x38 TM7 polar (hydrogen bond with backbone)
CCX662 Q301 7.39x38 TM7 polar (hydrogen bond)
CCX662 S304 7.42x41 TM7 Van der Waals
CCX662 L305 7.43x42 TM7 hydrophobic
CCX662 L305 7.43x42 TM7 Van der Waals

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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
TM1
1x39 1.39x39 Y51
TM2
2x60 2.60x60 W100
2x63 2.63x63 S103
2x64 2.64x64 L104
TM3
3x29 3.29x29 H121
3x32 3.32x32 F124
3x33 3.33x33 S125
3x36 3.36x36 L128
3x37 3.37x37 F129
3x40 3.40x40 I132
ECL2
45x51 45.51x51 R197
TM5
5x32 5.31x32 I205
5x33 5.32x33 K206
5x36 5.35x36 L209
5x43 5.42x43 S216
5x461 5.46x461 G220
TM6
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x52 6.52x52 H269
6x58 6.58x58 D275
6x62 6.62x62 I279
6x63 6.63x63 L280
6x64 6.64x64 H281
TM7
7x27 7.28x27 E290
7x30 7.31x30 L293
7x31 7.32x31 F294
7x34 7.35x34 L297
7x38 7.39x38 Q301
7x41 7.42x41 S304
7x42 7.43x42 L305