Go - Y2 receptor complex model

GPCR CLASS (FAMILY)

A (Rhodopsin)

SPECIES

Homo sapiens

G PROTEIN FAMILY

Gi/o

DATE

2024-05-15

3D VIEW

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


Tertiary structure confidence

Chain pLDDT score avg
Y2 79.7
Gαo 89.4
Gβ1 94.2
Gγ2 85.1
Very high (>90)
Confident (90-70)
Low (70-50)
Very low (<50)
Disordered

PTM Score: 0.8
iPTM Score: 0.8
PAE mean: 11.2


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 definitions:

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
Polar H8 N 331 8x49 G.H5 R 349 G.H5.21
Van-der-waals H8 N 331 8x49 G.H5 R 349 G.H5.21
Hydrophobic C-term V 381 - G.s3h2 G 203 G.s3h2.01
Van-der-waals C-term V 381 - G.s3h2 G 203 G.s3h2.01
Hydrophobic C-term V 381 - G.H2 R 209 G.H2.04
Van-der-waals C-term V 381 - G.H2 R 209 G.H2.04
Hydrophobic TM5 P 252 5x71 G.H5 D 337 G.H5.09
Ionic TM6 R 262 6x29 G.h4s6 E 318 G.h4s6.12
Polar TM6 R 262 6x29 G.h4s6 E 318 G.h4s6.12
Van-der-waals TM6 R 262 6x29 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM5 H 249 5x68 G.H5 I 344 G.H5.16
Van-der-waals TM5 H 249 5x68 G.H5 I 344 G.H5.16
Hydrophobic TM5 L 246 5x65 G.H5 L 348 G.H5.20
Polar C-term S 354 - G.H3 K 258 G.H3.16
Hydrophobic C-term S 354 - G.H3 K 258 G.H3.16
Van-der-waals C-term S 354 - G.H3 K 258 G.H3.16
Hydrophobic C-term V 381 - G.s1h1 G 40 G.s1h1.01
Van-der-waals C-term V 381 - G.s1h1 G 40 G.s1h1.01
Hydrophobic C-term T 379 - G.H3 L 250 G.H3.08
Polar ICL2 H 155 - G.H5 N 347 G.H5.19
Hydrophobic TM3 C 151 3x53 G.H5 C 351 G.H5.23
Van-der-waals TM3 C 151 3x53 G.H5 C 351 G.H5.23
Polar TM3 C 151 3x53 G.H5 C 351 G.H5.23
Hydrophobic TM5 H 249 5x68 G.H5 T 340 G.H5.12
Polar ICL2 K 159 - G.H5 N 347 G.H5.19
Hydrophobic ICL2 K 159 - G.H5 N 347 G.H5.19
Van-der-waals ICL2 K 159 - G.H5 N 347 G.H5.19
Hydrophobic TM5 P 252 5x71 G.H5 A 338 G.H5.10
Van-der-waals TM6 M 269 6x36 G.H5 G 352 G.H5.24
Hydrophobic TM6 L 270 6x37 G.H5 L 353 G.H5.25
Hydrophobic TM3 I 152 3x54 G.H5 N 347 G.H5.19
Van-der-waals TM3 I 152 3x54 G.H5 N 347 G.H5.19
Ionic C-term K 361 - G.H2 E 208 G.H2.03
Polar C-term K 361 - G.H2 E 208 G.H2.03
Van-der-waals C-term K 361 - G.H2 E 208 G.H2.03
Hydrophobic ICL3 A 254 - G.H4 E 309 G.H4.16
Polar TM6 Y 259 6x26 G.H5 D 341 G.H5.13
Hydrophobic TM6 Y 259 6x26 G.H5 D 341 G.H5.13
Van-der-waals TM6 Y 259 6x26 G.H5 D 341 G.H5.13
Hydrophobic TM5 L 246 5x65 G.H5 I 344 G.H5.16
Hydrophobic ICL2 L 156 - G.S3 L 195 G.S3.01
Van-der-waals ICL2 L 156 - G.S3 L 195 G.S3.01
Ionic TM5 H 249 5x68 G.H5 D 341 G.H5.13
Polar TM5 H 249 5x68 G.H5 D 341 G.H5.13
Hydrophobic TM5 H 249 5x68 G.H5 D 341 G.H5.13
Van-der-waals TM5 H 249 5x68 G.H5 D 341 G.H5.13
Hydrophobic ICL2 H 155 - G.H5 I 343 G.H5.15
Van-der-waals ICL2 H 155 - G.H5 I 343 G.H5.15
Polar TM3 C 151 3x53 G.H5 N 347 G.H5.19
Hydrophobic TM3 C 151 3x53 G.H5 N 347 G.H5.19
Van-der-waals TM3 C 151 3x53 G.H5 N 347 G.H5.19
Polar TM6 T 266 6x33 G.H5 L 353 G.H5.25
Hydrophobic TM6 T 266 6x33 G.H5 L 353 G.H5.25
Van-der-waals TM6 T 266 6x33 G.H5 L 353 G.H5.25
Hydrophobic ICL2 H 155 - G.H5 T 340 G.H5.12
Van-der-waals ICL2 H 155 - G.H5 T 340 G.H5.12
Hydrophobic TM5 G 253 5x72 G.S6 Y 320 G.S6.02
Van-der-waals TM5 G 253 5x72 G.S6 Y 320 G.S6.02
Hydrophobic TM3 R 148 3x50 G.H5 L 353 G.H5.25
Van-der-waals TM3 R 148 3x50 G.H5 L 353 G.H5.25
Hydrophobic TM5 P 252 5x71 G.S6 Y 320 G.S6.02
Van-der-waals TM5 P 252 5x71 G.S6 Y 320 G.S6.02
Polar H8 S 330 8x48 G.H5 Y 354 G.H5.26
Van-der-waals H8 S 330 8x48 G.H5 Y 354 G.H5.26
Polar TM6 R 262 6x29 G.h4s6 P 315 G.h4s6.09
Van-der-waals TM6 R 262 6x29 G.h4s6 P 315 G.h4s6.09
Hydrophobic C-term V 381 - G.H2 W 212 G.H2.07
Polar C-term V 381 - G.H1 K 46 G.H1.01
Hydrophobic C-term V 381 - G.H1 K 46 G.H1.01
Van-der-waals C-term V 381 - G.H1 K 46 G.H1.01
Polar TM3 R 148 3x50 G.H5 G 352 G.H5.24
Polar C-term T 379 - G.H2 R 209 G.H2.04
Van-der-waals C-term T 379 - G.H2 R 209 G.H2.04
Hydrophobic TM5 K 245 5x64 G.H5 I 344 G.H5.16
Van-der-waals TM5 K 245 5x64 G.H5 I 344 G.H5.16
Hydrophobic TM6 T 266 6x33 G.H5 L 348 G.H5.20
Hydrophobic TM6 M 269 6x36 G.H5 L 353 G.H5.25
Van-der-waals TM6 M 269 6x36 G.H5 L 353 G.H5.25
Hydrophobic C-term F 375 - G.H3 S 253 G.H3.11
Van-der-waals C-term F 375 - G.H3 S 253 G.H3.11
Polar TM5 S 251 5x70 G.H5 D 341 G.H5.13
Hydrophobic TM5 S 251 5x70 G.H5 D 341 G.H5.13
Van-der-waals TM5 S 251 5x70 G.H5 D 341 G.H5.13
Polar TM3 R 148 3x50 G.H5 C 351 G.H5.23
Hydrophobic TM3 R 148 3x50 G.H5 C 351 G.H5.23
Van-der-waals TM3 R 148 3x50 G.H5 C 351 G.H5.23
Hydrophobic TM2 T 85 2x39 G.H5 C 351 G.H5.23
Polar TM2 T 85 2x39 G.H5 C 351 G.H5.23
Hydrophobic C-term V 381 - G.S1 L 39 G.S1.07
Van-der-waals C-term V 381 - G.S1 L 39 G.S1.07
Polar C-term N 380 - G.H2 R 206 G.H2.01
Hydrophobic C-term N 380 - G.H2 R 206 G.H2.01
Van-der-waals C-term N 380 - G.H2 R 206 G.H2.01
Hydrophobic H8 N 329 8x47 G.H5 G 352 G.H5.24
Van-der-waals H8 N 329 8x47 G.H5 G 352 G.H5.24
Polar C-term N 380 - G.s4h3 E 237 G.s4h3.10
Van-der-waals C-term N 380 - G.s4h3 E 237 G.s4h3.10
Polar TM6 R 262 6x29 G.H5 Y 354 G.H5.26
Hydrophobic TM6 R 262 6x29 G.H5 Y 354 G.H5.26
Van-der-waals TM6 R 262 6x29 G.H5 Y 354 G.H5.26
Hydrophobic ICL2 H 155 - G.H5 I 344 G.H5.16
Hydrophobic TM3 I 152 3x54 G.H5 L 348 G.H5.20
Van-der-waals TM3 I 152 3x54 G.H5 L 348 G.H5.20
Hydrophobic TM5 P 252 5x71 G.H5 D 341 G.H5.13
Polar TM5 S 251 5x70 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM6 Y 259 6x26 G.h4s6 E 318 G.h4s6.12
Hydrophobic C-term H 350 - G.h3s5 I 261 G.h3s5.01
Van-der-waals C-term H 350 - G.h3s5 I 261 G.h3s5.01
Polar H8 N 331 8x49 G.H5 G 350 G.H5.22
Hydrophobic ICL2 L 156 - G.H5 I 343 G.H5.15
Hydrophobic TM3 I 152 3x54 G.H5 L 353 G.H5.25
Van-der-waals TM3 I 152 3x54 G.H5 L 353 G.H5.25
Hydrophobic C-term V 381 - G.H3 L 250 G.H3.08
Van-der-waals C-term V 381 - G.H3 L 250 G.H3.08
Polar C-term T 356 - G.H3 K 258 G.H3.16
Hydrophobic C-term A 378 - G.H2 R 206 G.H2.01
Hydrophobic C-term V 353 - G.H3 K 258 G.H3.16
Polar C-term N 380 - G.s1h1 G 42 G.s1h1.03
Hydrophobic C-term T 376 - G.H2 K 210 G.H2.05
Hydrophobic C-term T 379 - G.H3 E 246 G.H3.04
Polar TM6 K 265 6x32 G.H5 Y 354 G.H5.26
Van-der-waals TM6 K 265 6x32 G.H5 Y 354 G.H5.26
Hydrophobic C-term F 375 - G.H3 M 249 G.H3.07
Van-der-waals C-term F 375 - G.H3 M 249 G.H3.07
Hydrophobic C-term E 377 - G.s4h3 E 237 G.s4h3.10
Hydrophobic C-term F 375 - G.s4h3 D 238 G.s4h3.11