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SMTL ID : 8izb.1

Lysophosphatidylserine receptor GPR174-Gs complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

UBL.1:

20 residues within 4Å:

Chain E: Y.184, Y.188, I.229, I.230, A.233, C.234, F.237, L.240, R.241, V.255, M.270, I.277, Y.331, F.335, D.338, F.339, K.342, H.359
Ligands: SER.2, CLR.4

15 PLIP interactions:

15 interactions with chain E

Hydrophobic interactions: E:Y.188, E:I.229, E:I.230, E:F.237, E:F.237, E:L.240, E:I.277, E:F.335, E:F.339, E:F.339
Hydrogen bonds: E:Y.331, E:H.359
Salt bridges: E:R.241, E:R.241, E:K.342

1 x SER: SERINE(Non-covalent)

SER.2:

9 residues within 4Å:

Chain E: Y.107, R.160, Y.164, F.180, K.183, Y.184, F.254, L.363
Ligands: UBL.1

7 PLIP interactions:

7 interactions with chain E

Hydrogen bonds: E:Y.107, E:Y.111, E:Y.111, E:Y.184, E:Y.184
Salt bridges: E:R.160, E:K.183

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.3:	7 residues within 4Å: Chain E: I.144, N.145, I.148, L.152, L.220, W.227, C.231 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.144, E:I.148, E:L.152, E:W.227, E:W.227
CLR.4:	9 residues within 4Å: Chain E: Y.188, I.191, Y.192, V.195, C.196, I.222, I.277, P.282 Ligands: UBL.1 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.191, E:Y.192, E:Y.192, E:I.222, E:P.282

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

2023-11-01

Peptides

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short: 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
Nanobody35: D
Probable G-protein coupled receptor 174: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
N

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(s) subunit alpha isoforms short

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

Nanobody35

Probable G-protein coupled receptor 174

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

Background

Transparent

Resolution

Low
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High
Extreme

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