Rhodopsin - Gt1

GPCR CLASS (FAMILY)

Class A (Rhodopsin)

GPCR SPECIES

Bos taurus

GPCR PREFERRED CHAIN

R

G PROTEIN (FAMILY)

Gi/o

G PROTEIN SPECIES

Bos taurus

PDB CODE

6OY9

RESOLUTION

3.9 Å

REFERENCE

10.1016/J.MOLCEL.2019.06.007

PUBLICATION DATE

July 24, 2019

3D VIEW

NGL is a WebGL based 3D viewer powered by MMTF.

LIGAND INTERACTIONS

23 interactions (Click to see)

LIGANDS

Retinal (all-trans) - Agonist pubchem

PHYSIOLOGICAL LIGANDS

No physiological ligands available



GPCR - G protein interface interactions



The biflare plot is a modified version of a flareplot, where lines are drawn between an inner concentric circle (Gα residues) and an outer concentric circle (GPCR residues) depicting the interface interactions.
Different interaction types are shown with different line types (aromatic - solid, hydrophobic - dashed, ionic - long dashed, polar - dotted, Van der Waals - dash-dot).
The interactive features include filtering on interaction type, segments, residues and backbone or sidechain interactions.


Interaction cut-off:

Residue numbering:

GPCR-G protein backbone (bb) or sidechain (sc):





Structures

Sequence Color

Gα, Gβ, Gγ, GPCR
Interaction cut-off: strict (stick), loose (line)

NGL is a WebGL based 3D viewer powered by MMTF.

Interaction
type		 GPCR
Segment
AA
Number		 Generic
number		 Gα
segment
AA
Number		 Generic
number
Hydrophobic TM5 L 226 5x61 G.H5 L 349 G.H5.25
Van-der-waals TM5 L 226 5x61 G.H5 L 349 G.H5.25
Hydrophobic TM3 V 139 3x54 G.H5 L 344 G.H5.20
Van-der-waals TM3 V 139 3x54 G.H5 L 344 G.H5.20
Hydrophobic TM3 V 138 3x53 G.H5 C 347 G.H5.23
Hydrophobic ICL2 R 147 - G.hns1 R 28 G.hns1.03
Hydrophobic TM3 R 135 3x50 G.H5 C 347 G.H5.23
Polar TM6 T 242 6x25 G.H5 K 341 G.H5.17
Hydrophobic TM6 T 242 6x25 G.H5 K 341 G.H5.17
Van-der-waals TM6 T 242 6x25 G.H5 K 341 G.H5.17
Hydrophobic TM6 A 246 6x29 G.H5 F 350 G.H5.26
Van-der-waals TM6 A 246 6x29 G.H5 F 350 G.H5.26
Hydrophobic TM6 M 253 6x36 G.H5 L 349 G.H5.25
Polar ICL2 N 145 - G.hns1 R 28 G.hns1.03
Hydrophobic ICL2 N 145 - G.hns1 R 28 G.hns1.03
Van-der-waals ICL2 N 145 - G.hns1 R 28 G.hns1.03
Polar ICL4 K 311 - G.H5 F 350 G.H5.26
Aromatic ICL4 K 311 - G.H5 F 350 G.H5.26
Hydrophobic TM3 R 135 3x50 G.H5 L 349 G.H5.25
Van-der-waals TM3 R 135 3x50 G.H5 L 349 G.H5.25
Hydrophobic ICL1 L 72 - G.H5 C 347 G.H5.23
Van-der-waals ICL1 L 72 - G.H5 C 347 G.H5.23
Hydrophobic ICL3 Q 237 - G.H5 D 337 G.H5.13
Van-der-waals ICL3 Q 237 - G.H5 D 337 G.H5.13
Hydrophobic TM6 S 240 6x23 G.h4s6 E 314 G.h4s6.12
Van-der-waals TM6 S 240 6x23 G.h4s6 E 314 G.h4s6.12
Hydrophobic TM6 E 249 6x32 G.H5 F 350 G.H5.26
Polar TM6 T 242 6x25 G.h4s6 E 314 G.h4s6.12
Hydrophobic TM6 T 242 6x25 G.h4s6 E 314 G.h4s6.12
Van-der-waals TM6 T 242 6x25 G.h4s6 E 314 G.h4s6.12
Hydrophobic TM5 A 233 5x68 G.H5 I 340 G.H5.16
Hydrophobic TM6 V 250 6x33 G.H5 L 349 G.H5.25
Van-der-waals TM6 V 250 6x33 G.H5 L 349 G.H5.25
Polar ICL3 Q 237 - G.H5 D 333 G.H5.09
Hydrophobic TM5 T 229 5x64 G.H5 I 340 G.H5.16
Polar TM6 A 241 6x24 G.h4s6 E 314 G.h4s6.12
Van-der-waals TM6 A 241 6x24 G.h4s6 E 314 G.h4s6.12
Hydrophobic ICL2 K 141 - G.H5 I 339 G.H5.15
Van-der-waals ICL2 K 141 - G.H5 I 339 G.H5.15
Polar ICL4 N 310 - G.H5 C 347 G.H5.23
Hydrophobic ICL4 N 310 - G.H5 G 348 G.H5.24
Van-der-waals ICL4 N 310 - G.H5 G 348 G.H5.24
Polar ICL4 K 311 - G.H5 G 348 G.H5.24
Hydrophobic ICL4 K 311 - G.H5 G 348 G.H5.24
Van-der-waals ICL4 K 311 - G.H5 G 348 G.H5.24