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SMTL ID : 7ejx.1

Structure of the GPR88-Gi1 signaling complex bound to a synthetic ligand

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x J5F: (1R,2R)-N-[(2S,3S)-2-azanyl-3-methyl-pentyl]-N-[4-(4-propylphenyl)phenyl]-2-pyridin-2-yl-cyclopropane-1-carboxamide(Non-covalent)

J5F.1:

18 residues within 4Å:

Chain A: L.209, L.213, I.215, V.216, V.219, R.220, L.281, S.282, G.283, L.284, V.286, L.287, C.290
Chain B: L.348, L.353
Ligands: CLR.2, CLR.3, CLR.4

13 PLIP interactions:

11 interactions with chain A, 2 interactions with chain B

Hydrophobic interactions: A:L.213, A:I.215, A:V.216, A:V.216, A:V.219, A:L.281, A:L.284, A:V.286, A:V.286, A:L.287, B:L.348, B:L.353
Hydrogen bonds: A:S.282

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2:	6 residues within 4Å: Chain A: L.287, C.291, L.294 Ligands: J5F.1, CLR.3, CLR.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.294
CLR.3:	5 residues within 4Å: Chain A: L.209, L.213, L.294 Ligands: J5F.1, CLR.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.209, A:L.213, A:L.213, A:L.294
CLR.4:	6 residues within 4Å: Chain A: L.281, L.287, L.288, L.295 Ligands: J5F.1, CLR.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.281, A:L.288, A:L.295

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Chen, G. et al., Activation and allosteric regulation of the orphan GPR88-Gi1 signaling complex. Nat Commun (2022)

Release Date

2022-04-13

Peptides

Probable G-protein coupled receptor 88: A
Guanine nucleotide-binding protein G(i) subunit alpha-1: B
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: C
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: D
scFv16: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
A

C
B

D
G

E
S

Membrane

We predict this structure to be a membrane protein.
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Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Probable G-protein coupled receptor 88

Guanine nucleotide-binding protein G(i) subunit alpha-1

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

scFv16

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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