Rhodopsin - Gi1

GPCR CLASS (FAMILY)

Class A (Rhodopsin)

GPCR SPECIES

Homo sapiens

GPCR PREFERRED CHAIN

R

G PROTEIN (FAMILY)

Gi/o

G PROTEIN SPECIES

Homo sapiens

PDB CODE

RESOLUTION

4.5 Å

REFERENCE

PUBLICATION DATE

June 20, 2018

3D VIEW

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

LIGAND INTERACTIONS

LIGANDS

Apo (no ligand) - Apo (no ligand)

ENDOGENOUS LIGANDS

No endogenous 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 M 253 6x36 G.H5 L 353 G.H5.25
Van-der-waals TM6 M 253 6x36 G.H5 L 353 G.H5.25
Polar TM6 T 242 6x25 G.h4s6 D 315 G.h4s6.09
Hydrophobic TM3 V 139 3x54 G.H5 N 347 G.H5.19
Hydrophobic TM6 A 246 6x29 G.H5 F 354 G.H5.26
Van-der-waals TM6 A 246 6x29 G.H5 F 354 G.H5.26
Polar TM6 S 240 6x23 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM6 S 240 6x23 G.h4s6 E 318 G.h4s6.12
Van-der-waals TM6 S 240 6x23 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM6 E 249 6x32 G.H5 L 353 G.H5.25
Van-der-waals TM6 E 249 6x32 G.H5 L 353 G.H5.25
Ionic TM3 K 141 3x56 G.s2s3 D 193 G.s2s3.02
Hydrophobic TM6 A 246 6x29 G.H5 L 348 G.H5.20
Hydrophobic TM6 T 242 6x25 G.H5 F 354 G.H5.26
Van-der-waals TM6 T 242 6x25 G.H5 F 354 G.H5.26
Hydrophobic TM3 V 138 3x53 G.H5 C 351 G.H5.23
Hydrophobic ICL2 R 147 - G.hns1 R 32 G.hns1.03
Hydrophobic TM5 Q 237 5x72 G.H5 D 341 G.H5.13
Hydrophobic TM6 V 250 6x33 G.H5 L 353 G.H5.25
Van-der-waals TM7 M 309 7x56 G.H5 G 352 G.H5.24
Polar TM6 A 241 6x24 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM6 K 245 6x28 G.H5 F 354 G.H5.26
Polar H8 K 311 8x48 G.H5 G 352 G.H5.24
Hydrophobic TM6 E 249 6x32 G.H5 F 354 G.H5.26
Polar TM5 Q 237 5x72 G.S6 Y 320 G.S6.02
Hydrophobic TM3 R 135 3x50 G.H5 L 353 G.H5.25
Hydrophobic H8 N 310 8x47 G.H5 G 352 G.H5.24
Hydrophobic TM3 V 139 3x54 G.H5 C 351 G.H5.23
Hydrophobic TM3 V 139 3x54 G.H5 L 348 G.H5.20
Polar ICL2 R 147 - G.hns1 A 31 G.hns1.02
Polar H8 K 311 8x48 G.H5 F 354 G.H5.26
Hydrophobic H8 K 311 8x48 G.H5 F 354 G.H5.26
Van-der-waals H8 K 311 8x48 G.H5 F 354 G.H5.26
Polar TM6 S 240 6x23 G.H5 K 345 G.H5.17
Hydrophobic ICL3 E 239 - G.S6 Y 320 G.S6.02
Van-der-waals ICL3 E 239 - G.S6 Y 320 G.S6.02