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SMTL ID : 8wrb.1

Lysophosphatidylserine receptor GPR34-Gi complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.1:

4 residues within 4Å:

Chain E: N.148, I.151, L.155, W.232

5 PLIP interactions:

5 interactions with chain E

Hydrophobic interactions: E:I.151, E:L.155, E:W.232, E:W.232, E:W.232

1 x SER: SERINE(Non-covalent)

SER.2:

8 residues within 4Å:

Chain E: Y.188, F.258, H.259, R.339, Y.342, N.362, E.363
Ligands: UBL.3

6 PLIP interactions:

2 Ligand-Ligand interactions, 4 interactions with chain E

Hydrogen bonds: S.2, S.2, E:F.258, E:Y.342, E:N.362
Salt bridges: E:R.339

1 x UBL: [(2R)-2-oxidanyl-3-phosphonooxy-propyl] (Z)-octadec-9-enoate(Non-covalent)

UBL.3:

13 residues within 4Å:

Chain E: G.184, T.185, Y.188, L.234, A.235, G.238, M.242, F.258, R.261, N.273, L.276, M.279
Ligands: SER.2

7 PLIP interactions:

7 interactions with chain E

Hydrophobic interactions: E:T.185, E:Y.188, E:A.235
Hydrogen bonds: E:T.185, E:N.273
Salt bridges: E:R.261, E:K.263

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Liu, G. et al., Structural basis for ligand recognition and signaling of the lysophosphatidylserine receptors GPR34 and GPR174. Plos Biol. (2023)

Release Date

2023-11-08

Peptides

Guanine nucleotide-binding protein G(i) subunit alpha-1: A
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: B
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: C
Antibody fragment scFv16: D
Probable G-protein coupled receptor 34,Tag: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
R

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

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

Antibody fragment scFv16

Probable G-protein coupled receptor 34,Tag

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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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