PDB
7SK6
Resolution
4.0 Å
Released
July 27, 2022
Receptor
ACKR3
Class
A
Species
Homo sapiens
Ligand
CXCL12_LRHQ
Function
Agonist
Reference
10.1126/SCIADV.ABN8063

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Ligand Amino Acid Generic Number Segment Interaction Type
CXCL12_LRHQ I27 N-term polar (hydrogen bond)
CXCL12_LRHQ V28 N-term polar (hydrogen bond with backbone)
CXCL12_LRHQ V28 N-term Van der Waals
CXCL12_LRHQ V29 N-term polar (hydrogen bond)
CXCL12_LRHQ D30 N-term polar (charge-assisted hydrogen bond)
CXCL12_LRHQ D30 N-term polar (hydrogen bond with backbone)
CXCL12_LRHQ T31 N-term polar (hydrogen bond)
CXCL12_LRHQ V32 N-term polar (hydrogen bond)
CXCL12_LRHQ V32 N-term polar (hydrogen bond with backbone)
CXCL12_LRHQ M33 N-term polar (hydrogen bond)
CXCL12_LRHQ C34 N-term polar (hydrogen bond with backbone)
CXCL12_LRHQ C34 N-term polar (hydrogen bond)
CXCL12_LRHQ P35 N-term Van der Waals
CXCL12_LRHQ N36 N-term polar (hydrogen bond)
CXCL12_LRHQ N36 N-term polar (hydrogen bond with backbone)
CXCL12_LRHQ K40 N-term polar (charge-assisted hydrogen bond)
CXCL12_LRHQ Y51 1.39x39 TM1 polar (hydrogen bond)
CXCL12_LRHQ W100 2.60x60 TM2 polar (hydrogen bond with backbone)
CXCL12_LRHQ W100 2.60x60 TM2 polar (hydrogen bond)
CXCL12_LRHQ S103 2.63x63 TM2 polar (hydrogen bond)
CXCL12_LRHQ L104 2.64x64 TM2 Van der Waals
CXCL12_LRHQ H107 ECL1 Van der Waals
CXCL12_LRHQ N108 ECL1 polar (hydrogen bond)
CXCL12_LRHQ N108 ECL1 polar (hydrogen bond)
CXCL12_LRHQ C117 3.25x25 TM3 Van der Waals
CXCL12_LRHQ H121 3.29x29 TM3 polar (hydrogen bond)
CXCL12_LRHQ F124 3.32x32 TM3 polar (hydrogen bond)
CXCL12_LRHQ S125 3.33x33 TM3 Van der Waals
CXCL12_LRHQ L128 3.36x36 TM3 Van der Waals
CXCL12_LRHQ F129 3.37x37 TM3 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ D179 4.60x61 TM4 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ L183 4.64x65 TM4 hydrophobic
CXCL12_LRHQ L183 4.64x65 TM4 Van der Waals
CXCL12_LRHQ Y195 ECL2 polar (hydrogen bond)
CXCL12_LRHQ C196 45.50x50 ECL2 polar (hydrogen bond with backbone)
CXCL12_LRHQ C196 45.50x50 ECL2 Van der Waals
CXCL12_LRHQ R197 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ S198 45.52x52 ECL2 polar (hydrogen bond with backbone)
CXCL12_LRHQ S198 45.52x52 ECL2 polar (hydrogen bond)
CXCL12_LRHQ Y200 ECL2 polar (hydrogen bond)
CXCL12_LRHQ I205 5.31x32 TM5 polar (hydrogen bond)
CXCL12_LRHQ K206 5.32x33 TM5 polar (hydrogen bond with backbone)
CXCL12_LRHQ K206 5.32x33 TM5 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ L209 5.35x36 TM5 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ L209 5.35x36 TM5 polar (hydrogen bond with backbone)
CXCL12_LRHQ L209 5.35x36 TM5 polar (hydrogen bond)
CXCL12_LRHQ I210 5.36x37 TM5 Van der Waals
CXCL12_LRHQ M212 5.38x39 TM5 polar (hydrogen bond)
CXCL12_LRHQ E213 5.39x40 TM5 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ E213 5.39x40 TM5 polar (charge-charge)
CXCL12_LRHQ S216 5.42x43 TM5 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ S216 5.42x43 TM5 polar (hydrogen bond)
CXCL12_LRHQ W265 6.48x48 TM6 Van der Waals
CXCL12_LRHQ Y268 6.51x51 TM6 polar (hydrogen bond)
CXCL12_LRHQ H269 6.52x52 TM6 Van der Waals
CXCL12_LRHQ D275 6.58x58 TM6 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ D275 6.58x58 TM6 polar (charge-charge)
CXCL12_LRHQ I279 6.62x62 TM6 polar (hydrogen bond)
CXCL12_LRHQ I279 6.62x62 TM6 polar (hydrogen bond with backbone)
CXCL12_LRHQ L280 6.63x63 TM6 polar (hydrogen bond with backbone)
CXCL12_LRHQ L280 6.63x63 TM6 polar (hydrogen bond)
CXCL12_LRHQ H281 6.64x64 TM6 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ H281 6.64x64 TM6 polar (hydrogen bond)
CXCL12_LRHQ H281 6.64x64 TM6 polar (hydrogen bond with backbone)
CXCL12_LRHQ H281 6.64x64 TM6 polar (hydrogen bond)
CXCL12_LRHQ Y282 ECL3 polar (hydrogen bond)
CXCL12_LRHQ Y282 ECL3 polar (hydrogen bond)
CXCL12_LRHQ P284 ECL3 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ F285 ECL3 polar (hydrogen bond with backbone)
CXCL12_LRHQ F285 ECL3 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ E290 7.28x27 TM7 polar (hydrogen bond with backbone)
CXCL12_LRHQ E290 7.28x27 TM7 polar (charge-charge)
CXCL12_LRHQ E290 7.28x27 TM7 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ L293 7.31x30 TM7 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ F294 7.32x31 TM7 polar (hydrogen bond)
CXCL12_LRHQ F294 7.32x31 TM7 polar (charge-assisted hydrogen bond)
CXCL12_LRHQ F294 7.32x31 TM7 polar (hydrogen bond with backbone)
CXCL12_LRHQ L297 7.35x34 TM7 polar (hydrogen bond)
CXCL12_LRHQ H298 7.36x35 TM7 polar (hydrogen bond)
CXCL12_LRHQ Q301 7.39x38 TM7 polar (hydrogen bond)
CXCL12_LRHQ 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
TM1
1x39 1.39x39 Y51
TM2
2x60 2.60x60 W100
2x63 2.63x63 S103
2x64 2.64x64 L104
TM3
3x25 3.25x25 C117
3x29 3.29x29 H121
3x32 3.32x32 F124
3x33 3.33x33 S125
3x36 3.36x36 L128
3x37 3.37x37 F129
TM4
4x61 4.60x61 D179
4x65 4.64x65 L183
ECL2
45x50 45.50x50 C196
45x51 45.51x51 R197
45x52 45.52x52 S198
TM5
5x32 5.31x32 I205
5x33 5.32x33 K206
5x36 5.35x36 L209
5x37 5.36x37 I210
5x39 5.38x39 M212
5x40 5.39x40 E213
5x43 5.42x43 S216
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
7x35 7.36x35 H298
7x38 7.39x38 Q301