Structure information

Rhodopsin

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

6PEL

SPECIES

Bos taurus

RESOLUTION

3.190

PREFERRED CHAIN

A

REFERENCE

PUBLICATION DATE

June 24, 2020

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
Citronellol E122 3.37x37 TM3 polar (charge-assisted hydrogen bond)
Citronellol Y191 ECL2 hydrophobic
Citronellol Y191 ECL2 Van der Waals
Citronellol V204 5.39x40 TM5 hydrophobic
Citronellol V204 5.39x40 TM5 Van der Waals
Citronellol M207 5.42x43 TM5 hydrophobic
Citronellol M207 5.42x43 TM5 Van der Waals
Citronellol F208 5.43x44 TM5 hydrophobic
Citronellol H211 5.46x461 TM5 polar (hydrogen bond with backbone)
Citronellol H211 5.46x461 TM5 Van der Waals
Citronellol F212 5.47x47 TM5 hydrophobic
Citronellol W265 6.48x48 TM6 Van der Waals
Citronellol W265 6.48x48 TM6 hydrophobic
Citronellol Y268 6.51x51 TM6 hydrophobic
Citronellol Y268 6.51x51 TM6 Van der Waals
Citronellol A269 6.52x52 TM6 hydrophobic
Citronellol A269 6.52x52 TM6 Van der Waals
Citronellol A272 6.55x55 TM6 hydrophobic
Citronellol A272 6.55x55 TM6 Van der Waals
Citronellol F273 6.56x56 TM6 Van der Waals

Ligands

Citronellol

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Residue Diagrams

F N I P F G L M I L L F M Y A A L M S F 1 L N L A V A D L F M V G F G F T T T L Y T 2 V V L S W L A I E G G L T A F F G E L N 3 A I M G V A F T W V M A L A C A A P P L 4 Y C F F I V I L P I I F H V V F M Y I V F 5 I I M V I A F L I C W L P Y A G V A F Y 6 V P N Y V A S T K A F F A P I T M F I 7
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ICL1 K K L R ICL1ECL1 Y F V F ECL1ICL2 P M S N F R F ICL2ECL2 W S R Y I P E G M Q C S C G I D Y Y T P H E E T ECL2ICL3 Q E ICL3ECL3 Q G S D F ECL3N-term M N G T E G P N F Y V P F S N K T G V V R S P F E A P Q Y Y L A N-termC-term C G K N P L G D D E A S T T V S K T E T S Q V A P A C-term E P W Q F S M L A A Y M F L L I M L G F P I N F L T L Y V T V Q H T P L N Y I L L N L A V A D L F M V F G G F T T T L Y T S L H G G P T G C N L E G F F A T L G G E I A L W S L V V L A I E R Y V V V C K G E N H A I M G V A F T W V M A L A C A A P P L V G N N E S F V I Y M F V V H F I I P L I V I F F C Y G Q L V F T V K E A A A Q Q S A T T Q K A E K E V T R M V I I M V I A F L I C W L P Y A G V A F Y I F T H G P I F M T I P A F F A K T S A V Y N P V I Y I M M N K Q M V T F R N C T L C
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Residue Table


GPCRdb(A)
GPCRdb(A)
Rhodopsin
TM3
3x37 3.37x37 E122
TM5
5x40 5.39x40 V204
5x43 5.42x43 M207
5x44 5.43x44 F208
5x461 5.46x461 H211
5x47 5.47x47 F212
TM6
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x52 6.52x52 A269
6x55 6.55x55 A272
6x56 6.56x56 F273