PDB
5WB2
Resolution
3.5 Å
Released
June 13, 2018
Receptor
US28
Class
A
Species
Human cytomegalovirus
Ligand
CX3CL1.35
Function
Agonist
Reference
10.7554/ELIFE.35850

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Ligand Amino Acid Generic Number Segment Interaction Type
CX3CL1.35 D17 N-term polar (charge-assisted hydrogen bond)
CX3CL1.35 E18 N-term Van der Waals
CX3CL1.35 A20 N-term Van der Waals
CX3CL1.35 T21 N-term Van der Waals
CX3CL1.35 P22 N-term Van der Waals
CX3CL1.35 P22 N-term hydrophobic
CX3CL1.35 C23 N-term Van der Waals
CX3CL1.35 C23 N-term polar (hydrogen bond with backbone)
CX3CL1.35 V24 N-term Van der Waals
CX3CL1.35 F25 1.24x24 TM1 polar (hydrogen bond with backbone)
CX3CL1.35 F25 1.24x24 TM1 Van der Waals
CX3CL1.35 L29 1.28x28 TM1 hydrophobic
CX3CL1.35 L29 1.28x28 TM1 Van der Waals
CX3CL1.35 S32 1.31x31 TM1 Van der Waals
CX3CL1.35 K33 1.32x32 TM1 Van der Waals
CX3CL1.35 T36 1.35x35 TM1 polar (hydrogen bond)
CX3CL1.35 W89 2.60x60 TM2 Van der Waals
CX3CL1.35 L93 2.64x64 TM2 hydrophobic
CX3CL1.35 T108 3.29x29 TM3 Van der Waals
CX3CL1.35 F111 3.32x32 TM3 Van der Waals
CX3CL1.35 F111 3.32x32 TM3 hydrophobic
CX3CL1.35 V166 ECL2 Van der Waals
CX3CL1.35 V166 ECL2 hydrophobic
CX3CL1.35 D170 ECL2 polar (hydrogen bond with backbone)
CX3CL1.35 D170 ECL2 polar (charge-assisted hydrogen bond)
CX3CL1.35 M174 45.51x51 ECL2 polar (hydrogen bond)
CX3CL1.35 T175 45.52x52 ECL2 polar (hydrogen bond with backbone)
CX3CL1.35 T175 45.52x52 ECL2 polar (hydrogen bond)
CX3CL1.35 T175 45.52x52 ECL2 polar (hydrogen bond)
CX3CL1.35 Y177 ECL2 Van der Waals
CX3CL1.35 D178 ECL2 polar (charge-assisted hydrogen bond)
CX3CL1.35 N189 5.39x40 TM5 polar (hydrogen bond)
CX3CL1.35 L192 5.42x43 TM5 Van der Waals
CX3CL1.35 L192 5.42x43 TM5 hydrophobic
CX3CL1.35 Y244 6.51x51 TM6 polar (hydrogen bond)
CX3CL1.35 Y244 6.51x51 TM6 polar (hydrogen bond)
CX3CL1.35 L248 6.55x55 TM6 Van der Waals
CX3CL1.35 L248 6.55x55 TM6 hydrophobic
CX3CL1.35 D251 6.58x58 TM6 Van der Waals
CX3CL1.35 L255 6.62x62 TM6 Van der Waals
CX3CL1.35 E266 7.28x27 TM7 Van der Waals
CX3CL1.35 K270 7.32x31 TM7 polar (charge-assisted hydrogen bond)
CX3CL1.35 L273 7.35x34 TM7 hydrophobic
CX3CL1.35 L273 7.35x34 TM7 Van der Waals
CX3CL1.35 I274 7.36x35 TM7 Van der Waals
CX3CL1.35 I274 7.36x35 TM7 hydrophobic
CX3CL1.35 E277 7.39x38 TM7 polar (charge-assisted hydrogen bond)
CX3CL1.35 F281 7.43x42 TM7 Van der Waals
CX3CL1.35 F281 7.43x42 TM7 hydrophobic

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Snake plot — Download: PNG | SVG
ICL1 R R I Q ICL1ECL1 H N S L ECL1ICL2 Y 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 G 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 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
1x31 1.31x31 S32
1x32 1.32x32 K33
1x35 1.35x35 T36
TM2
2x60 2.60x60 W89
2x64 2.64x64 L93
TM3
3x29 3.29x29 T108
3x32 3.32x32 F111
ECL2
45x51 45.51x51 M174
45x52 45.52x52 T175
TM5
5x40 5.39x40 N189
5x43 5.42x43 L192
TM6
6x51 6.51x51 Y244
6x55 6.55x55 L248
6x58 6.58x58 D251
6x62 6.62x62 L255
TM7
7x27 7.28x27 E266
7x31 7.32x31 K270
7x34 7.35x34 L273
7x35 7.36x35 I274
7x38 7.39x38 E277
7x42 7.43x42 F281