Gz - P2Y13 receptor complex model

GPCR CLASS (FAMILY)

A (Rhodopsin)

SPECIES

Homo sapiens

G PROTEIN FAMILY

Gi/o

DATE

2023-09-15

3D VIEW

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


Tertiary structure confidence

Chain pLDDT score avg
P2Y13 78.1
Gαz 83.1
Very high (>90)
Confident (90-70)
Low (70-50)
Very low (<50)
Disordered

PTM Score: 0.6
iPTM Score: 0.4
PAE mean: 19.1


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, 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 C-term T 352 - G.H3 S 253 G.H3.11
Van-der-waals C-term T 352 - G.H3 S 253 G.H3.11
Polar TM7 L 320 7x56 G.H5 C 355 G.H5.26
Hydrophobic TM7 L 320 7x56 G.H5 C 355 G.H5.26
Van-der-waals TM7 L 320 7x56 G.H5 C 355 G.H5.26
Polar TM5 S 238 5x68 G.H5 Q 346 G.H5.17
Polar TM7 L 320 7x56 G.H5 G 353 G.H5.24
Hydrophobic TM7 L 320 7x56 G.H5 G 353 G.H5.24
Van-der-waals TM7 L 320 7x56 G.H5 G 353 G.H5.24
Polar TM7 L 320 7x56 G.H5 L 354 G.H5.25
Hydrophobic TM7 L 320 7x56 G.H5 L 354 G.H5.25
Van-der-waals TM7 L 320 7x56 G.H5 L 354 G.H5.25
Hydrophobic TM2 F 78 2x39 G.H5 C 355 G.H5.26
Van-der-waals TM2 F 78 2x39 G.H5 C 355 G.H5.26
Hydrophobic ICL2 L 149 34x51 G.H5 F 337 G.H5.08
Van-der-waals ICL2 L 149 34x51 G.H5 F 337 G.H5.08
Polar TM5 Y 239 5x69 G.H5 Q 346 G.H5.17
Hydrophobic TM5 Y 239 5x69 G.H5 Q 346 G.H5.17
Van-der-waals TM5 Y 239 5x69 G.H5 Q 346 G.H5.17
Hydrophobic ICL3 S 242 - G.S6 Y 321 G.S6.02
Van-der-waals ICL3 S 242 - G.S6 Y 321 G.S6.02
Hydrophobic C-term L 353 - G.H2 W 212 G.H2.07
Van-der-waals C-term L 353 - G.H2 W 212 G.H2.07
Van-der-waals ICL2 P 148 34x50 G.H5 N 348 G.H5.19
Polar ICL3 S 242 - G.h4s6 E 319 G.h4s6.12
Hydrophobic ICL3 S 242 - G.h4s6 E 319 G.h4s6.12
Van-der-waals ICL3 S 242 - G.h4s6 E 319 G.h4s6.12
Hydrophobic TM6 V 257 6x38 G.H5 L 349 G.H5.20
Van-der-waals TM6 V 257 6x38 G.H5 L 349 G.H5.20
Hydrophobic C-term I 351 - G.H2 I 213 G.H2.08
Van-der-waals C-term I 351 - G.H2 I 213 G.H2.08
Hydrophobic ICL2 L 149 34x51 G.S3 L 195 G.S3.01
Van-der-waals ICL2 L 149 34x51 G.S3 L 195 G.S3.01
Polar ICL2 N 151 34x53 G.hns1 R 32 G.hns1.03
Hydrophobic ICL2 N 151 34x53 G.hns1 R 32 G.hns1.03
Van-der-waals ICL2 N 151 34x53 G.hns1 R 32 G.hns1.03
Van-der-waals ICL3 S 242 - G.S6 I 320 G.S6.01
Hydrophobic ICL2 L 149 34x51 G.H5 I 344 G.H5.15
Van-der-waals ICL2 L 149 34x51 G.H5 I 344 G.H5.15
Hydrophobic ICL2 P 148 34x50 G.H5 I 345 G.H5.16
Polar H8 K 323 8x49 G.H5 C 355 G.H5.26
Hydrophobic H8 K 323 8x49 G.H5 C 355 G.H5.26
Van-der-waals H8 K 323 8x49 G.H5 C 355 G.H5.26
Hydrophobic H8 C 321 8x47 G.H5 L 354 G.H5.25
Polar TM6 D 246 6x27 G.h4s6 E 316 G.h4s6.09
Hydrophobic TM6 D 246 6x27 G.h4s6 E 316 G.h4s6.09
Van-der-waals TM6 D 246 6x27 G.h4s6 E 316 G.h4s6.09
Polar TM6 N 249 6x30 G.h4s6 E 316 G.h4s6.09
Hydrophobic TM6 N 249 6x30 G.h4s6 E 316 G.h4s6.09
Van-der-waals TM6 N 249 6x30 G.h4s6 E 316 G.h4s6.09
Hydrophobic TM5 S 238 5x68 G.H5 D 342 G.H5.13
Hydrophobic TM3 I 145 3x54 G.H5 I 352 G.H5.23
Van-der-waals TM3 I 145 3x54 G.H5 I 352 G.H5.23
Hydrophobic TM6 L 253 6x34 G.H5 K 350 G.H5.21
Van-der-waals TM6 L 253 6x34 G.H5 K 350 G.H5.21
Polar C-term G 354 - G.H2 R 209 G.H2.04
Hydrophobic C-term G 354 - G.H2 R 209 G.H2.04
Van-der-waals C-term G 354 - G.H2 R 209 G.H2.04
Van-der-waals H8 K 322 8x48 G.H5 C 355 G.H5.26
Polar C-term N 350 - G.H3 N 257 G.H3.15
Hydrophobic C-term N 350 - G.H3 N 257 G.H3.15
Van-der-waals C-term N 350 - G.H3 N 257 G.H3.15
Hydrophobic H8 K 322 8x48 G.H5 L 354 G.H5.25
Van-der-waals H8 K 322 8x48 G.H5 L 354 G.H5.25
Hydrophobic ICL2 L 149 34x51 G.S1 I 34 G.S1.02
Van-der-waals ICL2 L 149 34x51 G.S1 I 34 G.S1.02
Hydrophobic TM5 Y 239 5x69 G.h4s6 E 319 G.h4s6.12
Van-der-waals TM5 Y 239 5x69 G.h4s6 E 319 G.h4s6.12
Polar H8 K 322 8x48 G.H5 G 353 G.H5.24
Polar C-term N 350 - G.H3 N 258 G.H3.16
Hydrophobic C-term N 350 - G.H3 N 258 G.H3.16
Hydrophobic TM2 L 82 2x43 G.H5 C 355 G.H5.26
Van-der-waals TM2 L 82 2x43 G.H5 C 355 G.H5.26
Hydrophobic C-term L 353 - G.H2 R 209 G.H2.04
Van-der-waals C-term L 353 - G.H2 R 209 G.H2.04
Hydrophobic TM3 K 144 3x53 G.H5 I 352 G.H5.23
Hydrophobic TM5 V 235 5x65 G.H5 L 349 G.H5.20
Van-der-waals TM5 V 235 5x65 G.H5 L 349 G.H5.20
Hydrophobic TM3 I 145 3x54 G.H5 L 349 G.H5.20
Van-der-waals TM3 I 145 3x54 G.H5 L 349 G.H5.20
Hydrophobic C-term T 348 - G.H3 N 258 G.H3.16
Van-der-waals C-term T 348 - G.H3 N 258 G.H3.16
Hydrophobic ICL2 P 148 34x50 G.H5 I 344 G.H5.15
Van-der-waals ICL2 P 148 34x50 G.H5 I 344 G.H5.15
Hydrophobic TM6 D 246 6x27 G.h4s6 K 315 G.h4s6.08
Van-der-waals TM6 D 246 6x27 G.h4s6 K 315 G.h4s6.08
Van-der-waals TM2 F 78 2x39 G.H5 I 352 G.H5.23
Hydrophobic C-term L 353 - G.h2s4 F 216 G.h2s4.01
Van-der-waals TM7 L 320 7x56 G.H5 I 352 G.H5.23
Polar TM6 K 243 6x24 G.H4 Q 305 G.H4.12
Hydrophobic TM6 K 243 6x24 G.H4 Q 305 G.H4.12
Van-der-waals TM6 K 243 6x24 G.H4 Q 305 G.H4.12
Hydrophobic TM3 I 145 3x54 G.H5 I 345 G.H5.16
Van-der-waals TM3 I 145 3x54 G.H5 I 345 G.H5.16
Polar TM3 R 141 3x50 G.H5 I 352 G.H5.23
Hydrophobic TM3 R 141 3x50 G.H5 I 352 G.H5.23
Van-der-waals TM3 R 141 3x50 G.H5 I 352 G.H5.23
Ionic ICL3 K 241 - G.H5 D 342 G.H5.13
Polar ICL3 K 241 - G.H5 D 342 G.H5.13
Hydrophobic ICL3 K 241 - G.H5 D 342 G.H5.13
Van-der-waals ICL3 K 241 - G.H5 D 342 G.H5.13
Ionic ICL3 K 241 - G.H5 D 338 G.H5.09
Hydrophobic ICL2 L 149 34x51 G.H5 T 341 G.H5.12
Van-der-waals ICL2 L 149 34x51 G.H5 T 341 G.H5.12
Hydrophobic TM6 L 253 6x34 G.H5 L 349 G.H5.20
Polar H8 C 321 8x47 G.H5 C 355 G.H5.26
Hydrophobic H8 C 321 8x47 G.H5 C 355 G.H5.26
Van-der-waals H8 C 321 8x47 G.H5 C 355 G.H5.26
Ionic ICL2 R 150 34x52 G.s2s3 E 194 G.s2s3.02
Polar ICL2 R 150 34x52 G.s2s3 E 194 G.s2s3.02
Hydrophobic ICL2 R 150 34x52 G.s2s3 E 194 G.s2s3.02
Van-der-waals ICL2 R 150 34x52 G.s2s3 E 194 G.s2s3.02
Polar H8 C 321 8x47 G.H5 G 353 G.H5.24
Hydrophobic H8 C 321 8x47 G.H5 G 353 G.H5.24
Van-der-waals H8 C 321 8x47 G.H5 G 353 G.H5.24
Hydrophobic C-term L 353 - G.H3 I 254 G.H3.12
Van-der-waals C-term L 353 - G.H3 I 254 G.H3.12
Hydrophobic C-term G 354 - G.H2 R 206 G.H2.01
Van-der-waals C-term G 354 - G.H2 R 206 G.H2.01
Hydrophobic TM2 I 79 2x40 G.H5 C 355 G.H5.26
Van-der-waals TM2 I 79 2x40 G.H5 C 355 G.H5.26
Hydrophobic C-term N 350 - G.H3 W 259 G.H3.17
Van-der-waals C-term N 350 - G.H3 W 259 G.H3.17
Hydrophobic TM6 S 244 6x25 G.h4s6 E 319 G.h4s6.12
Polar TM3 K 144 3x53 G.H5 N 348 G.H5.19
Hydrophobic TM3 K 144 3x53 G.H5 N 348 G.H5.19
Van-der-waals TM3 K 144 3x53 G.H5 N 348 G.H5.19
Hydrophobic ICL2 P 148 34x50 G.H5 T 341 G.H5.12
Polar TM6 S 244 6x25 G.h4s6 K 315 G.h4s6.08