G13 - Rhodopsin complex model

GPCR CLASS (FAMILY)

A (Rhodopsin)

SPECIES

Homo sapiens

G PROTEIN FAMILY

G12/13

DATE

2023-09-15

3D VIEW

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


Tertiary structure confidence

(pLDDT score) avg.: 83.9

Very high (>90)
Confident (90-70)
Low (70-50)
Very low (<50)
Disordered

PTM Score: 0.6
iPTM Score: 0.4
PAE mean: 20.6


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, 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 TM3 V 139 3x54 G.H5 L 374 G.H5.23
Van-der-waals TM3 V 139 3x54 G.H5 L 374 G.H5.23
Hydrophobic ICL2 M 143 34x51 G.HN K 42 G.HN.51
Hydrophobic ICL2 S 144 34x52 G.hns1 K 46 G.hns1.02
Van-der-waals ICL2 S 144 34x52 G.hns1 K 46 G.hns1.02
Ionic TM5 E 232 5x67 G.hns1 R 47 G.hns1.03
Polar TM5 E 232 5x67 G.hns1 R 47 G.hns1.03
Hydrophobic TM5 E 232 5x67 G.hns1 R 47 G.hns1.03
Van-der-waals TM5 E 232 5x67 G.hns1 R 47 G.hns1.03
Hydrophobic ICL2 S 144 34x52 G.hns1 V 45 G.hns1.01
Ionic ICL3 E 239 - G.H5 K 363 G.H5.12
Polar ICL3 E 239 - G.H5 K 363 G.H5.12
Van-der-waals ICL3 E 239 - G.H5 K 363 G.H5.12
Polar TM3 K 141 3x56 G.hns1 K 46 G.hns1.02
Hydrophobic TM3 K 141 3x56 G.hns1 K 46 G.hns1.02
Van-der-waals TM3 K 141 3x56 G.hns1 K 46 G.hns1.02
Polar ICL2 M 143 34x51 G.hns1 K 46 G.hns1.02
Hydrophobic ICL2 M 143 34x51 G.hns1 K 46 G.hns1.02
Van-der-waals ICL2 M 143 34x51 G.hns1 K 46 G.hns1.02
Polar ICL2 R 147 34x55 G.h3s5 S 282 G.h3s5.01
Hydrophobic ICL2 S 144 34x52 G.HN K 42 G.HN.51
Van-der-waals ICL2 S 144 34x52 G.HN K 42 G.HN.51
Polar C-term S 343 - G.H4 R 331 G.H4.16
Hydrophobic C-term S 343 - G.H4 R 331 G.H4.16
Van-der-waals C-term S 343 - G.H4 R 331 G.H4.16
Hydrophobic TM6 V 250 6x33 G.H5 L 371 G.H5.20
Hydrophobic TM6 T 243 6x26 G.H5 L 371 G.H5.20
Van-der-waals C-term S 343 - G.H4 V 327 G.H4.12
Hydrophobic TM5 Q 237 5x72 G.H5 K 363 G.H5.12
Van-der-waals TM5 Q 237 5x72 G.H5 K 363 G.H5.12
Hydrophobic TM6 E 249 6x32 G.H5 M 375 G.H5.24
Van-der-waals TM6 E 249 6x32 G.H5 M 375 G.H5.24
Polar TM5 Q 236 5x71 G.s2s3 N 215 G.s2s3.02
Hydrophobic TM5 Q 236 5x71 G.s2s3 N 215 G.s2s3.02
Van-der-waals TM5 Q 236 5x71 G.s2s3 N 215 G.s2s3.02
Hydrophobic H8 Q 312 8x49 G.H5 Q 377 G.H5.26
Van-der-waals H8 Q 312 8x49 G.H5 Q 377 G.H5.26
Hydrophobic TM6 M 253 6x36 G.H5 M 375 G.H5.24
Hydrophobic ICL1 K 67 12x49 G.h4s6 Q 339 G.h4s6.13
Van-der-waals ICL1 K 67 12x49 G.h4s6 Q 339 G.h4s6.13
Polar ICL1 K 67 12x49 G.h4s6 Q 338 G.h4s6.12
Hydrophobic ICL1 K 67 12x49 G.h4s6 Q 338 G.h4s6.12
Van-der-waals ICL1 K 67 12x49 G.h4s6 Q 338 G.h4s6.12
Hydrophobic TM5 L 226 5x61 G.H5 L 374 G.H5.23
Polar C-term T 340 - G.S6 H 345 G.S6.04
Hydrophobic C-term T 340 - G.S6 H 345 G.S6.04
Van-der-waals C-term T 340 - G.S6 H 345 G.S6.04
Polar TM6 E 249 6x32 G.H5 Q 377 G.H5.26
Van-der-waals TM6 E 249 6x32 G.H5 Q 377 G.H5.26
Hydrophobic C-term V 345 - G.H4 E 328 G.H4.13
Van-der-waals C-term V 345 - G.H4 E 328 G.H4.13
Hydrophobic TM6 A 246 6x29 G.H5 L 371 G.H5.20
Van-der-waals TM6 A 246 6x29 G.H5 L 371 G.H5.20
Hydrophobic ICL3 E 239 - G.H5 R 360 G.H5.09
Ionic ICL3 E 239 - G.s2s3 K 214 G.s2s3.01
Polar ICL3 E 239 - G.s2s3 K 214 G.s2s3.01
Hydrophobic ICL3 E 239 - G.s2s3 K 214 G.s2s3.01
Van-der-waals ICL3 E 239 - G.s2s3 K 214 G.s2s3.01
Polar TM5 Q 236 5x71 G.S3 V 216 G.S3.01
Hydrophobic TM5 Q 236 5x71 G.S3 V 216 G.S3.01
Van-der-waals TM5 Q 236 5x71 G.S3 V 216 G.S3.01
Hydrophobic TM6 V 250 6x33 G.H5 M 375 G.H5.24
Van-der-waals TM6 V 250 6x33 G.H5 M 375 G.H5.24
Ionic C-term E 341 - G.H4 R 320 G.H4.05
Polar C-term E 341 - G.H4 R 320 G.H4.05
Hydrophobic C-term E 341 - G.H4 R 320 G.H4.05
Van-der-waals C-term E 341 - G.H4 R 320 G.H4.05
Polar ICL2 P 142 34x50 G.hns1 K 46 G.hns1.02
Hydrophobic ICL2 P 142 34x50 G.hns1 K 46 G.hns1.02
Van-der-waals ICL2 P 142 34x50 G.hns1 K 46 G.hns1.02
Hydrophobic TM5 Q 237 5x72 G.H5 L 367 G.H5.16
Van-der-waals TM5 Q 237 5x72 G.H5 L 367 G.H5.16
Hydrophobic TM5 V 230 5x65 G.H5 L 371 G.H5.20
Van-der-waals TM5 V 230 5x65 G.H5 L 371 G.H5.20
Polar ICL3 S 240 - G.H5 D 364 G.H5.13
Hydrophobic ICL3 S 240 - G.H5 D 364 G.H5.13
Van-der-waals ICL3 S 240 - G.H5 D 364 G.H5.13
Polar TM5 Q 236 5x71 G.s2s3 K 214 G.s2s3.01
Hydrophobic TM5 Q 236 5x71 G.s2s3 K 214 G.s2s3.01
Van-der-waals TM5 Q 236 5x71 G.s2s3 K 214 G.s2s3.01
Hydrophobic TM2 L 72 2x39 G.H5 L 376 G.H5.25
Hydrophobic TM3 R 135 3x50 G.H5 L 376 G.H5.25
Van-der-waals TM3 R 135 3x50 G.H5 L 376 G.H5.25
Polar C-term E 341 - G.S6 H 344 G.S6.03
Hydrophobic C-term E 341 - G.S6 H 344 G.S6.03
Van-der-waals C-term E 341 - G.S6 H 344 G.S6.03
Hydrophobic C-term V 345 - G.H4 R 331 G.H4.16
Van-der-waals C-term V 345 - G.H4 R 331 G.H4.16
Polar H8 N 310 8x47 G.H5 L 376 G.H5.25
Hydrophobic H8 N 310 8x47 G.H5 L 376 G.H5.25
Van-der-waals H8 N 310 8x47 G.H5 L 376 G.H5.25
Hydrophobic C-term T 342 - G.S6 H 344 G.S6.03
Van-der-waals C-term T 342 - G.S6 H 344 G.S6.03
Hydrophobic H8 K 311 8x48 G.H5 Q 377 G.H5.26
Hydrophobic TM5 A 233 5x68 G.H5 L 367 G.H5.16
Polar C-term S 338 - G.H5 D 361 G.H5.10
Hydrophobic C-term S 338 - G.H5 D 361 G.H5.10
Van-der-waals C-term S 338 - G.H5 D 361 G.H5.10
Van-der-waals ICL2 N 145 34x53 G.hns1 V 45 G.hns1.01
Polar ICL2 R 147 34x55 G.h3s5 N 283 G.h3s5.02
Hydrophobic ICL2 R 147 34x55 G.h3s5 N 283 G.h3s5.02
Van-der-waals ICL2 R 147 34x55 G.h3s5 N 283 G.h3s5.02
Polar TM6 T 242 6x25 G.H5 D 364 G.H5.13
Hydrophobic TM2 L 76 2x43 G.H5 L 376 G.H5.25
Hydrophobic TM5 V 230 5x65 G.H5 L 374 G.H5.23
Hydrophobic TM3 L 131 3x46 G.H5 L 376 G.H5.25
Van-der-waals TM3 L 131 3x46 G.H5 L 376 G.H5.25