PDB
7RKF
Resolution
4.0 Å
Released
Jan. 26, 2022
Receptor
US28
Class
A
Species
Human cytomegalovirus
Ligand
Function
Fractalkine
Agonist
Reference
10.1126/SCIADV.ABL5442

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Ligand Amino Acid Generic Number Segment Interaction Type
Fractalkine D15 N-term hydrophobic
Fractalkine E18 N-term hydrophobic
Fractalkine E18 N-term polar (charge-charge)
Fractalkine A20 N-term hydrophobic
Fractalkine P22 N-term hydrophobic
Fractalkine C23 N-term Van der Waals
Fractalkine V24 N-term Van der Waals
Fractalkine F25 1.24x24 TM1 Van der Waals
Fractalkine L29 1.28x28 TM1 Van der Waals
Fractalkine K33 1.32x32 TM1 Van der Waals
Fractalkine Y40 1.39x39 TM1 polar (hydrogen bond)
Fractalkine W89 2.60x60 TM2 hydrophobic
Fractalkine W89 2.60x60 TM2 aromatic (edge-to-face)
Fractalkine L93 2.64x64 TM2 hydrophobic
Fractalkine T108 3.29x29 TM3 hydrophobic
Fractalkine F111 3.32x32 TM3 Van der Waals
Fractalkine Y112 3.33x33 TM3 Van der Waals
Fractalkine D170 ECL2 Van der Waals
Fractalkine Q172 ECL2 Van der Waals
Fractalkine M174 45.51x51 ECL2 Van der Waals
Fractalkine D178 ECL2 polar (hydrogen bond)
Fractalkine D178 ECL2 polar (charge-charge)
Fractalkine L273 7.35x34 TM7 hydrophobic
Fractalkine I274 7.36x35 TM7 Van der Waals
Fractalkine E277 7.39x38 TM7 Van der Waals

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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
1x32 1.32x32 K33
1x39 1.39x39 Y40
TM2
2x60 2.60x60 W89
2x64 2.64x64 L93
TM3
3x29 3.29x29 T108
3x32 3.32x32 F111
3x33 3.33x33 Y112
ECL2
45x51 45.51x51 M174
TM7
7x34 7.35x34 L273
7x35 7.36x35 I274
7x38 7.39x38 E277