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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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8ge2.1 | 8ge3.1 | 8ge4.1 | 8ge5.1 | 8ge6.1 | 8ge7.1 | 8ge8.1 | 8ge9.1 | 8gea.1 | 8geb.1 | 8gec.1 | 8ged.1 | 8gee.1 | 8gef.1 | 8geg.1 | 8geh.1 | 8gei.1 | 8gej.1 | 8gfv.1 | 8gfw.1 | 8gfx.1 | 8gfy.1 | 8gfz.1 | 8gg0.1 | 8gg1.1 | 8gg2.1 | 8gg3.1 | 8gg4.1 | 8gg5.1 | 8gg6.1 | 8gg7.1 | 8gg8.1 | 8gg9.1 | 8gga.1 | 8ggb.1 | 8ggc.1 | 8gge.1 | 8ggf.1 | 8ghv.1 | 8guq.1 | 8gur.1 | 8gus.1 | 8gut.1 | 8gy7.1 | 8h0p.1 | 8h0q.1 | 8h2g.1 | 8h4i.1 | 8h4k.1 | 8h4l.1 | 8h8j.1 | 8ha0.1 | 8haf.1 | 8hao.1 | 8hbd.1 | 8hcq.1 | 8hcx.1 | 8hdo.1 | 8hdp.1 | 8hj5.1 | 8hn8.1 | 8hnk.1 | 8hnl.1 | 8hnm.1 | 8hoc.1 | 8hqc.1 | 8hsc.1 | 8hti.1 | 8i2g.1 | 8i7v.1 | 8i7w.1 | 8i95.1 | 8i97.1 | 8i9a.1 | 8i9l.1 | 8i9s.1 | 8ia2.1 | 8ia8.1 | 8ic0.1 | 8id3.1 | 8id4.1 | 8id6.1 | 8id8.1 | 8id9.1 | 8iec.1 | 8ied.1 | 8ikg.1 | 8ikh.1 | 8ikl.1 | 8inr.1 | 8ioc.1 | 8iod.1 | 8iq4.1 | 8iq6.1 | 8irs.1 | 8irt.1 | 8iru.1 | 8irv.1 | 8itl.1 | 8itm.1 | 8iu2.1 | 8iuk.1 | 8iul.1 | 8ium.1 | 8iy5.1 | 8iy9.1 | 8iyh.1 | 8iys.1 | 8iyw.1 | 8iz4.1 | 8izb.1 | 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9avg.1 | 9avl.1 | 9axf.1 | 9ayf.1 | 9bkk.1 | 9bqj.1 | 9dqh.1 | 9dqj.1 | 9erx.1 | 9gyo.1 | 9iyb.1 | 9j5v.1 | 9k1c.1 | 9k1d.1

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

Background

Transparent

Resolution

Low
Medium
High
Extreme

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