Structure information

Rhodopsin

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

5WKT

SPECIES

Bos taurus

RESOLUTION

3.200

PREFERRED CHAIN

A

REFERENCE

10.1038/NPROT.2017.135

PUBLICATION DATE

Dec. 13, 2017

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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
B-Octylglucoside T118 3.33x33 TM3 polar (hydrogen bond)
B-Octylglucoside T118 3.33x33 TM3 polar (hydrogen bond with backbone)
B-Octylglucoside T118 3.33x33 TM3 polar (hydrogen bond)
B-Octylglucoside G121 3.36x36 TM3 Van der Waals
B-Octylglucoside E122 3.37x37 TM3 polar (charge-assisted hydrogen bond)
B-Octylglucoside C187 45.50x50 ECL2 polar (hydrogen bond with backbone)
B-Octylglucoside C187 45.50x50 ECL2 Van der Waals
B-Octylglucoside G188 45.51x51 ECL2 Van der Waals
B-Octylglucoside I189 45.52x52 ECL2 polar (hydrogen bond with backbone)
B-Octylglucoside I189 45.52x52 ECL2 Van der Waals
B-Octylglucoside Y191 ECL2 hydrophobic
B-Octylglucoside Y191 ECL2 Van der Waals
B-Octylglucoside M207 5.42x43 TM5 Van der Waals
B-Octylglucoside M207 5.42x43 TM5 hydrophobic
B-Octylglucoside F208 5.43x44 TM5 Van der Waals
B-Octylglucoside F212 5.47x47 TM5 Van der Waals
B-Octylglucoside W265 6.48x48 TM6 Van der Waals
B-Octylglucoside W265 6.48x48 TM6 hydrophobic
B-Octylglucoside Y268 6.51x51 TM6 polar (hydrogen bond)
B-Octylglucoside Y268 6.51x51 TM6 polar (hydrogen bond)
B-Octylglucoside A269 6.52x52 TM6 Van der Waals
B-Octylglucoside A269 6.52x52 TM6 polar (hydrogen bond with backbone)
B-Octylglucoside A272 6.55x55 TM6 Van der Waals

Ligands

B-Octylglucoside

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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
3x33 3.33x33 T118
3x36 3.36x36 G121
3x37 3.37x37 E122
ECL2
45x50 45.50x50 C187
45x51 45.51x51 G188
45x52 45.52x52 I189
TM5
5x43 5.42x43 M207
5x44 5.43x44 F208
5x47 5.47x47 F212
TM6
6x48 6.48x48 W265
6x51 6.51x51 Y268
6x52 6.52x52 A269
6x55 6.55x55 A272