PDB
7SK3
Resolution
3.8 Å
Released
July 27, 2022
Receptor
ACKR3
Class
A
Species
Homo sapiens
Ligand
[125I]CXCL12α (human)
Function
Agonist
Reference
10.1126/SCIADV.ABN8063

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Ligand Amino Acid Generic Number Segment Interaction Type
[125I]CXCL12α (human) I27 N-term polar (hydrogen bond)
[125I]CXCL12α (human) V28 N-term polar (hydrogen bond)
[125I]CXCL12α (human) V28 N-term polar (hydrogen bond with backbone)
[125I]CXCL12α (human) V29 N-term hydrophobic
[125I]CXCL12α (human) V29 N-term Van der Waals
[125I]CXCL12α (human) D30 N-term polar (charge-assisted hydrogen bond)
[125I]CXCL12α (human) D30 N-term polar (hydrogen bond with backbone)
[125I]CXCL12α (human) T31 N-term polar (hydrogen bond)
[125I]CXCL12α (human) V32 N-term polar (hydrogen bond with backbone)
[125I]CXCL12α (human) V32 N-term polar (hydrogen bond)
[125I]CXCL12α (human) M33 N-term polar (hydrogen bond)
[125I]CXCL12α (human) C34 N-term polar (hydrogen bond)
[125I]CXCL12α (human) C34 N-term polar (hydrogen bond with backbone)
[125I]CXCL12α (human) M37 N-term Van der Waals
[125I]CXCL12α (human) W100 2.60x60 TM2 hydrophobic
[125I]CXCL12α (human) W100 2.60x60 TM2 Van der Waals
[125I]CXCL12α (human) S103 2.63x63 TM2 polar (hydrogen bond)
[125I]CXCL12α (human) N108 ECL1 polar (hydrogen bond)
[125I]CXCL12α (human) W110 23.50x50 ECL1 Van der Waals
[125I]CXCL12α (human) C117 3.25x25 TM3 polar (hydrogen bond)
[125I]CXCL12α (human) C117 3.25x25 TM3 polar (hydrogen bond with backbone)
[125I]CXCL12α (human) H121 3.29x29 TM3 polar (hydrogen bond)
[125I]CXCL12α (human) F124 3.32x32 TM3 Van der Waals
[125I]CXCL12α (human) D179 4.60x61 TM4 Van der Waals
[125I]CXCL12α (human) L183 4.64x65 TM4 Van der Waals
[125I]CXCL12α (human) S188 ECL2 polar (hydrogen bond)
[125I]CXCL12α (human) S188 ECL2 polar (hydrogen bond)
[125I]CXCL12α (human) S190 ECL2 Van der Waals
[125I]CXCL12α (human) N191 ECL2 polar (hydrogen bond)
[125I]CXCL12α (human) N191 ECL2 polar (hydrogen bond)
[125I]CXCL12α (human) Y195 ECL2 aromatic (face-to-edge)
[125I]CXCL12α (human) Y195 ECL2 Van der Waals
[125I]CXCL12α (human) C196 45.50x50 ECL2 polar (hydrogen bond with backbone)
[125I]CXCL12α (human) C196 45.50x50 ECL2 Van der Waals
[125I]CXCL12α (human) R197 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
[125I]CXCL12α (human) S198 45.52x52 ECL2 polar (hydrogen bond)
[125I]CXCL12α (human) Y200 ECL2 polar (charge-assisted hydrogen bond)
[125I]CXCL12α (human) Y200 ECL2 polar (hydrogen bond)
[125I]CXCL12α (human) I205 5.31x32 TM5 polar (hydrogen bond)
[125I]CXCL12α (human) K206 5.32x33 TM5 Van der Waals
[125I]CXCL12α (human) L209 5.35x36 TM5 Van der Waals
[125I]CXCL12α (human) E213 5.39x40 TM5 Van der Waals
[125I]CXCL12α (human) Y268 6.51x51 TM6 polar (hydrogen bond)
[125I]CXCL12α (human) Y268 6.51x51 TM6 polar (hydrogen bond)
[125I]CXCL12α (human) D275 6.58x58 TM6 polar (charge-charge)
[125I]CXCL12α (human) D275 6.58x58 TM6 polar (charge-assisted hydrogen bond)
[125I]CXCL12α (human) I279 6.62x62 TM6 polar (hydrogen bond)
[125I]CXCL12α (human) I279 6.62x62 TM6 polar (hydrogen bond with backbone)
[125I]CXCL12α (human) L280 6.63x63 TM6 polar (hydrogen bond)
[125I]CXCL12α (human) L280 6.63x63 TM6 polar (hydrogen bond with backbone)
[125I]CXCL12α (human) H281 6.64x64 TM6 polar (hydrogen bond)
[125I]CXCL12α (human) H281 6.64x64 TM6 polar (hydrogen bond)
[125I]CXCL12α (human) Y282 ECL3 polar (charge-assisted hydrogen bond)
[125I]CXCL12α (human) Y282 ECL3 polar (hydrogen bond)
[125I]CXCL12α (human) F285 ECL3 hydrophobic
[125I]CXCL12α (human) F285 ECL3 Van der Waals
[125I]CXCL12α (human) E290 7.28x27 TM7 polar (charge-assisted hydrogen bond)
[125I]CXCL12α (human) L297 7.35x34 TM7 polar (hydrogen bond with backbone)
[125I]CXCL12α (human) L297 7.35x34 TM7 polar (hydrogen bond)
[125I]CXCL12α (human) L297 7.35x34 TM7 polar (charge-assisted hydrogen bond)
[125I]CXCL12α (human) H298 7.36x35 TM7 polar (hydrogen bond)
[125I]CXCL12α (human) 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
ECL1
23x50 23.50x50 W110
TM3
3x25 3.25x25 C117
3x29 3.29x29 H121
3x32 3.32x32 F124
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
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
7x27 7.28x27 E290
7x34 7.35x34 L297
7x35 7.36x35 H298
7x38 7.39x38 Q301