Rhodopsin - Go

GPCR CLASS (FAMILY)

Class A (Rhodopsin)

GPCR SPECIES

Bos taurus

GPCR PREFERRED CHAIN

A

G PROTEIN (FAMILY)

Gi/o

G PROTEIN SPECIES

Homo sapiens

PDB CODE

RESOLUTION

3.1 Å

REFERENCE

PUBLICATION DATE

Oct. 3, 2018

3D VIEW

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

LIGAND INTERACTIONS

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

, 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 T 242 6x25 G.h4s6 N 316 G.h4s6.10
Polar TM6 S 240 6x23 G.H5 D 341 G.H5.13
Hydrophobic TM6 S 240 6x23 G.H5 D 341 G.H5.13
Van-der-waals TM6 S 240 6x23 G.H5 D 341 G.H5.13
Polar TM6 S 240 6x23 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM6 S 240 6x23 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM6 K 245 6x28 G.H5 Y 354 G.H5.26
Van-der-waals TM6 K 245 6x28 G.H5 Y 354 G.H5.26
Polar H8 N 310 8x47 G.H5 C 351 G.H5.23
Hydrophobic TM5 Q 237 5x72 G.H5 D 341 G.H5.13
Hydrophobic TM3 R 135 3x50 G.H5 L 353 G.H5.25
Polar TM6 T 243 6x26 G.H5 D 341 G.H5.13
Hydrophobic TM6 T 243 6x26 G.H5 D 341 G.H5.13
Van-der-waals TM6 T 243 6x26 G.H5 D 341 G.H5.13
Hydrophobic ICL1 L 72 - G.H5 G 350 G.H5.22
Hydrophobic H8 Q 312 8x49 G.H5 G 352 G.H5.24
Hydrophobic TM6 A 246 6x29 G.H5 L 348 G.H5.20
Van-der-waals TM6 A 246 6x29 G.H5 L 348 G.H5.20
Hydrophobic TM6 Y 257 6x40 G.H5 L 353 G.H5.25
Van-der-waals TM6 Y 257 6x40 G.H5 L 353 G.H5.25
Polar TM6 T 242 6x25 G.H5 Y 354 G.H5.26
Hydrophobic TM6 T 242 6x25 G.H5 Y 354 G.H5.26
Van-der-waals TM6 T 242 6x25 G.H5 Y 354 G.H5.26
Hydrophobic TM5 L 226 5x61 G.H5 L 348 G.H5.20
Hydrophobic TM5 L 226 5x61 G.H5 L 353 G.H5.25
Hydrophobic TM5 A 233 5x68 G.H5 I 344 G.H5.16
Hydrophobic TM3 V 139 3x54 G.H5 I 344 G.H5.16
Polar H8 Q 312 8x49 G.H5 R 349 G.H5.21
Van-der-waals H8 Q 312 8x49 G.H5 R 349 G.H5.21
Hydrophobic H8 K 311 8x48 G.H5 Y 354 G.H5.26
Van-der-waals H8 K 311 8x48 G.H5 Y 354 G.H5.26
Hydrophobic TM6 M 253 6x36 G.H5 L 353 G.H5.25
Polar TM6 S 240 6x23 G.S6 Y 320 G.S6.02
Hydrophobic TM6 S 240 6x23 G.S6 Y 320 G.S6.02
Hydrophobic TM5 V 230 5x65 G.H5 L 348 G.H5.20
Hydrophobic TM5 Q 237 5x72 G.S6 Y 320 G.S6.02
Van-der-waals TM5 Q 237 5x72 G.S6 Y 320 G.S6.02
Polar TM6 K 245 6x28 G.h4s6 N 316 G.h4s6.10
Van-der-waals TM6 K 245 6x28 G.h4s6 N 316 G.h4s6.10
Hydrophobic TM3 V 139 3x54 G.H5 N 347 G.H5.19
Polar TM6 A 241 6x24 G.h4s6 E 318 G.h4s6.12
Van-der-waals TM6 A 241 6x24 G.h4s6 E 318 G.h4s6.12
Hydrophobic ICL1 L 72 - G.H5 C 351 G.H5.23
Hydrophobic TM3 V 139 3x54 G.H5 C 351 G.H5.23
Hydrophobic TM6 A 246 6x29 G.H5 Y 354 G.H5.26
Van-der-waals TM6 A 246 6x29 G.H5 Y 354 G.H5.26
Hydrophobic TM6 V 250 6x33 G.H5 L 348 G.H5.20
Polar TM3 V 138 3x53 G.H5 N 347 G.H5.19
Hydrophobic TM3 V 138 3x53 G.H5 N 347 G.H5.19
Hydrophobic TM6 E 249 6x32 G.H5 Y 354 G.H5.26
Hydrophobic TM5 T 229 5x64 G.H5 I 344 G.H5.16
Hydrophobic TM3 V 139 3x54 G.H5 L 348 G.H5.20
Hydrophobic H8 N 310 8x47 G.H5 G 352 G.H5.24
Van-der-waals H8 N 310 8x47 G.H5 G 352 G.H5.24
Polar TM6 T 242 6x25 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM6 T 242 6x25 G.h4s6 E 318 G.h4s6.12
Van-der-waals TM6 T 242 6x25 G.h4s6 E 318 G.h4s6.12
Polar TM3 R 135 3x50 G.H5 C 351 G.H5.23
Hydrophobic TM3 R 135 3x50 G.H5 C 351 G.H5.23
Van-der-waals TM3 R 135 3x50 G.H5 C 351 G.H5.23
Hydrophobic TM3 V 138 3x53 G.H5 C 351 G.H5.23
Polar H8 K 311 8x48 G.H5 G 352 G.H5.24
Hydrophobic H8 K 311 8x48 G.H5 G 352 G.H5.24
Van-der-waals H8 K 311 8x48 G.H5 G 352 G.H5.24
Hydrophobic TM6 V 250 6x33 G.H5 L 353 G.H5.25