Rhodopsin - Gi1

GPCR CLASS (FAMILY)

Class A (Rhodopsin)

GPCR SPECIES

Hasarius adansoni

GPCR PREFERRED CHAIN

R

G PROTEIN (FAMILY)

Gi/o

G PROTEIN SPECIES

Homo sapiens

PDB CODE

RESOLUTION

4.2 Å

REFERENCE

PUBLICATION DATE

Oct. 23, 2024

3D VIEW

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

LIGAND INTERACTIONS

LIGANDS

11,20-Ethanoretinal - 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

, , , 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

segment

AA

Number
Generic
number
Hydrophobic TM6 L 275 6x33 G.H5 L 348 G.H5.20
Van-der-waals TM6 L 275 6x33 G.H5 L 348 G.H5.20
Polar ICL2 M 156 - G.hns1 R 31 G.hns1.02
Hydrophobic ICL2 M 156 - G.hns1 R 31 G.hns1.02
Van-der-waals ICL2 M 156 - G.hns1 R 31 G.hns1.02
Hydrophobic TM7 S 334 7x56 G.H5 L 353 G.H5.25
Polar TM5 H 244 5x68 G.H5 C 337 G.H5.09
Hydrophobic TM5 H 244 5x68 G.H5 C 337 G.H5.09
Van-der-waals TM5 H 244 5x68 G.H5 C 337 G.H5.09
Hydrophobic TM6 L 275 6x33 G.H5 L 353 G.H5.25
Ionic ICL3 K 258 - G.H4 E 298 G.H4.05
Polar ICL3 K 258 - G.H4 E 298 G.H4.05
Hydrophobic ICL3 K 258 - G.H4 E 298 G.H4.05
Van-der-waals ICL3 K 258 - G.H4 E 298 G.H4.05
Hydrophobic ICL2 M 156 - G.H5 F 336 G.H5.08
Ionic TM5 H 244 5x68 G.H5 D 341 G.H5.13
Polar TM5 H 244 5x68 G.H5 D 341 G.H5.13
Hydrophobic TM5 H 244 5x68 G.H5 D 341 G.H5.13
Hydrophobic TM5 M 255 5x79 G.S6 F 323 G.S6.05
Van-der-waals TM3 R 148 3x50 G.H5 N 352 G.H5.24
Hydrophobic ICL2 M 156 - G.H5 K 340 G.H5.12
Hydrophobic ICL3 I 257 - G.H4 A 301 G.H4.08
Polar TM7 S 334 7x56 G.H5 N 352 G.H5.24
Hydrophobic TM7 S 334 7x56 G.H5 N 352 G.H5.24
Van-der-waals TM7 S 334 7x56 G.H5 N 352 G.H5.24
Polar TM6 R 274 6x32 G.H5 V 354 G.H5.26
Hydrophobic TM6 R 274 6x32 G.H5 V 354 G.H5.26
Van-der-waals TM6 R 274 6x32 G.H5 V 354 G.H5.26
Ionic ICL2 K 159 - G.HN E 28 G.HN.52
Polar ICL2 K 159 - G.HN E 28 G.HN.52
Hydrophobic ICL2 K 159 - G.HN E 28 G.HN.52
Van-der-waals ICL2 K 159 - G.HN E 28 G.HN.52
Polar H8 H 335 8x47 G.H5 N 352 G.H5.24
Hydrophobic H8 H 335 8x47 G.H5 N 352 G.H5.24
Van-der-waals H8 H 335 8x47 G.H5 N 352 G.H5.24
Hydrophobic ICL2 M 156 - G.H5 I 343 G.H5.15
Van-der-waals ICL2 M 156 - G.H5 I 343 G.H5.15
Polar TM5 H 244 5x68 G.H5 K 340 G.H5.12
Aromatic TM5 H 244 5x68 G.H5 K 340 G.H5.12
Hydrophobic TM5 H 244 5x68 G.H5 K 340 G.H5.12
Van-der-waals TM5 H 244 5x68 G.H5 K 340 G.H5.12
Polar H8 H 335 8x47 G.H5 C 351 G.H5.23
Hydrophobic TM6 R 274 6x32 G.H5 K 349 G.H5.21
Van-der-waals TM6 R 274 6x32 G.H5 K 349 G.H5.21
Hydrophobic ICL2 M 156 - G.S3 I 194 G.S3.01
Van-der-waals ICL2 M 156 - G.S3 I 194 G.S3.01
Polar TM5 S 247 5x71 G.H5 Q 333 G.H5.05
Polar TM6 R 274 6x32 G.H5 Q 345 G.H5.17
Ionic H8 K 337 8x49 G.H5 E 350 G.H5.22
Polar H8 K 337 8x49 G.H5 E 350 G.H5.22
Van-der-waals H8 K 337 8x49 G.H5 E 350 G.H5.22
Hydrophobic TM5 V 241 5x65 G.H5 L 344 G.H5.16
Polar TM5 Q 251 5x75 G.H5 K 330 G.H5.02
Hydrophobic TM5 Q 251 5x75 G.H5 K 330 G.H5.02
Hydrophobic TM3 I 152 3x54 G.H5 L 348 G.H5.20
Hydrophobic ICL3 I 257 - G.H4 E 298 G.H4.05
Van-der-waals ICL3 I 257 - G.H4 E 298 G.H4.05
Hydrophobic TM6 R 274 6x32 G.H5 L 348 G.H5.20
Van-der-waals TM6 R 274 6x32 G.H5 L 348 G.H5.20
Hydrophobic TM5 Q 251 5x75 G.H5 F 334 G.H5.06
Hydrophobic TM5 Q 251 5x75 G.S6 H 322 G.S6.04
Van-der-waals TM5 Q 251 5x75 G.S6 H 322 G.S6.04
Hydrophobic TM6 V 278 6x36 G.H5 L 353 G.H5.25
Hydrophobic TM3 I 152 3x54 G.H5 N 347 G.H5.19