PDB
2Z73
Resolution
2.5 Å
Released
May 13, 2008
Receptor
Rhodopsin
Class
A
Species
Todarodes pacificus
Ligand
Function
all-trans-retinal
Inverse agonist
Reference
10.1038/NATURE06925

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Ligand Amino Acid Generic Number Segment Interaction Type
all-trans-retinal N87 2.57x57 TM2 Van der Waals
all-trans-retinal Y111 3.28x28 TM3 hydrophobic
all-trans-retinal G112 3.29x29 TM3 Van der Waals
all-trans-retinal G115 3.32x32 TM3 Van der Waals
all-trans-retinal G116 3.33x33 TM3 Van der Waals
all-trans-retinal G119 3.36x36 TM3 Van der Waals
all-trans-retinal F120 3.37x37 TM3 hydrophobic
all-trans-retinal I123 3.40x40 TM3 Van der Waals
all-trans-retinal N185 ECL2 Van der Waals
all-trans-retinal C186 45.50x50 ECL2 Van der Waals
all-trans-retinal S187 45.51x51 ECL2 Van der Waals
all-trans-retinal F188 45.52x52 ECL2 hydrophobic
all-trans-retinal M204 5.42x43 TM5 hydrophobic
all-trans-retinal F205 5.43x44 TM5 hydrophobic
all-trans-retinal F209 5.47x47 TM5 hydrophobic
all-trans-retinal F270 6.44x44 TM6 Van der Waals
all-trans-retinal W274 6.48x48 TM6 hydrophobic
all-trans-retinal Y277 6.51x51 TM6 hydrophobic
all-trans-retinal A278 6.52x52 TM6 hydrophobic
all-trans-retinal V301 7.39x38 TM7 Van der Waals
all-trans-retinal K305 7.43x42 TM7 covalent bond

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

GPCRdb(A)
GPCRdb(A)
Rhodopsin
TM2
2x57 2.57x57 N87
TM3
3x28 3.28x28 Y111
3x29 3.29x29 G112
3x32 3.32x32 G115
3x33 3.33x33 G116
3x36 3.36x36 G119
3x37 3.37x37 F120
3x40 3.40x40 I123
ECL2
45x50 45.50x50 C186
45x51 45.51x51 S187
45x52 45.52x52 F188
TM5
5x43 5.42x43 M204
5x44 5.43x44 F205
5x47 5.47x47 F209
TM6
6x44 6.44x44 F270
6x48 6.48x48 W274
6x51 6.51x51 Y277
6x52 6.52x52 A278
TM7
7x38 7.39x38 V301
7x42 7.43x42 K305