PDB
8K3Z
Resolution
2.8 Å
Released
July 17, 2024
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
CXCL12
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
CXCL12 P27 N-term hydrophobic
CXCL12 C28 N-term polar (hydrogen bond with backbone)
CXCL12 C28 N-term Van der Waals
CXCL12 F29 N-term hydrophobic
CXCL12 F29 N-term Van der Waals
CXCL12 R30 N-term Van der Waals
CXCL12 Y45 1.39x39 TM1 Van der Waals
CXCL12 W94 2.60x60 TM2 Van der Waals
CXCL12 W94 2.60x60 TM2 hydrophobic
CXCL12 H113 3.29x29 TM3 Van der Waals
CXCL12 Y116 3.32x32 TM3 Van der Waals
CXCL12 Y116 3.32x32 TM3 hydrophobic
CXCL12 S178 ECL2 polar (hydrogen bond)
CXCL12 S178 ECL2 Van der Waals
CXCL12 I185 ECL2 hydrophobic
CXCL12 I185 ECL2 Van der Waals
CXCL12 C186 45.50x50 ECL2 polar (hydrogen bond with backbone)
CXCL12 C186 45.50x50 ECL2 Van der Waals
CXCL12 D187 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
CXCL12 F189 ECL2 Van der Waals
CXCL12 F189 ECL2 hydrophobic
CXCL12 Y190 ECL2 Van der Waals
CXCL12 Y190 ECL2 polar (hydrogen bond with backbone)
CXCL12 I259 6.55x55 TM6 hydrophobic
CXCL12 I259 6.55x55 TM6 Van der Waals
CXCL12 D262 6.58x58 TM6 polar (charge-assisted hydrogen bond)
CXCL12 L266 6.62x62 TM6 Van der Waals
CXCL12 E268 6.64x64 TM6 Van der Waals
CXCL12 H281 7.32x31 TM7 polar (hydrogen bond)
CXCL12 H281 7.32x31 TM7 Van der Waals
CXCL12 S285 7.36x35 TM7 Van der Waals
CXCL12 E288 7.39x38 TM7 polar (charge-assisted hydrogen bond)
CXCL12 F292 7.43x42 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
CXCR4
TM1
1x39 1.39x39 Y45
TM2
2x60 2.60x60 W94
TM3
3x29 3.29x29 H113
3x32 3.32x32 Y116
ECL2
45x50 45.50x50 C186
45x51 45.51x51 D187
TM6
6x55 6.55x55 I259
6x58 6.58x58 D262
6x62 6.62x62 L266
6x64 6.64x64 E268
TM7
7x31 7.32x31 H281
7x35 7.36x35 S285
7x38 7.39x38 E288
7x42 7.43x42 F292