PDB
7RKM
Resolution
3.5 Å
Released
Jan. 26, 2022
Receptor
US28
Class
A
Species
Human cytomegalovirus
Ligand
Function
Fractalkine
Agonist (partial)
Reference
10.1126/SCIADV.ABL5442

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Ligand Amino Acid Generic Number Segment Interaction Type
Fractalkine Y16 N-term hydrophobic
Fractalkine D17 N-term hydrophobic
Fractalkine E18 N-term Van der Waals
Fractalkine D19 N-term Van der Waals
Fractalkine A20 N-term polar (hydrogen bond with backbone)
Fractalkine T21 N-term Van der Waals
Fractalkine P22 N-term hydrophobic
Fractalkine C23 N-term polar (hydrogen bond with backbone)
Fractalkine V24 N-term hydrophobic
Fractalkine F25 1.24x24 TM1 polar (hydrogen bond with backbone)
Fractalkine L29 1.28x28 TM1 Van der Waals
Fractalkine Y40 1.39x39 TM1 polar (hydrogen bond)
Fractalkine W89 2.60x60 TM2 aromatic (edge-to-face)
Fractalkine W89 2.60x60 TM2 hydrophobic
Fractalkine Y92 2.63x63 TM2 polar (hydrogen bond with backbone)
Fractalkine Y92 2.63x63 TM2 aromatic (pi-cation)
Fractalkine Y92 2.63x63 TM2 hydrophobic
Fractalkine L93 2.64x64 TM2 hydrophobic
Fractalkine T108 3.29x29 TM3 Van der Waals
Fractalkine F111 3.32x32 TM3 hydrophobic
Fractalkine Y112 3.33x33 TM3 polar (hydrogen bond)
Fractalkine H162 4.60x61 TM4 Van der Waals
Fractalkine V166 ECL2 Van der Waals
Fractalkine Q172 ECL2 Van der Waals
Fractalkine C173 45.50x50 ECL2 Van der Waals
Fractalkine M174 45.51x51 ECL2 hydrophobic
Fractalkine T175 45.52x52 ECL2 hydrophobic
Fractalkine D176 ECL2 Van der Waals
Fractalkine Y177 ECL2 Van der Waals
Fractalkine D178 ECL2 Van der Waals
Fractalkine L248 6.55x55 TM6 Van der Waals
Fractalkine K270 7.32x31 TM7 polar (hydrogen bond)
Fractalkine L273 7.35x34 TM7 hydrophobic
Fractalkine I274 7.36x35 TM7 Van der Waals
Fractalkine E277 7.39x38 TM7 Van der Waals
Fractalkine F281 7.43x42 TM7 aromatic (edge-to-face)

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

GPCRdb(A)
GPCRdb(A)
US28
TM1
1x24 1.24x24 F25
1x28 1.28x28 L29
1x39 1.39x39 Y40
TM2
2x60 2.60x60 W89
2x63 2.63x63 Y92
2x64 2.64x64 L93
TM3
3x29 3.29x29 T108
3x32 3.32x32 F111
3x33 3.33x33 Y112
TM4
4x61 4.60x61 H162
ECL2
45x50 45.50x50 C173
45x51 45.51x51 M174
45x52 45.52x52 T175
TM6
6x55 6.55x55 L248
TM7
7x31 7.32x31 K270
7x34 7.35x34 L273
7x35 7.36x35 I274
7x38 7.39x38 E277
7x42 7.43x42 F281