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SMTL ID : 8zw0.1

Cryo-EM strcuture of Prostaglandin D2 Receptor DP1 activated by PGD2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1:	7 residues within 4Å: Chain C: S.231, Q.234, A.235, F.238, L.289, A.293, F.296 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Q.234, C:A.235, C:F.238, C:L.289, C:A.293, C:F.296, C:F.296 Hydrogen bonds: C:Q.234
CLR.2:	9 residues within 4Å: Chain C: M.191, C.194, G.195, V.198, T.199, F.239, F.242, F.243, S.285 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:M.191, C:V.198, C:F.242, C:F.243

1 x PG2: PROSTAGLANDIN D2(Non-covalent)

PG2.3:

16 residues within 4Å:

Chain C: G.151, L.154, F.155, K.204, L.207, S.208, V.211, Y.215, M.240, T.309, W.310, L.434, R.438, L.440, S.441, S.444

11 PLIP interactions:

11 interactions with chain C

Hydrophobic interactions: C:L.207, C:L.207, C:V.211, C:W.310, C:L.434, C:L.440
Hydrogen bonds: C:K.204, C:T.309, C:W.310, C:S.444
Salt bridges: C:R.438

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Xu, J. et al., Molecular Basis for Ligand Recognition and Receptor Activation of the Prostaglandin D2 Receptor DP1. To Be Published

Release Date

2025-05-28

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
Soluble cytochrome b562,Prostaglandin D2 receptor: C
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: D
nanobody Nb35: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
G

E
N

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

Soluble cytochrome b562,Prostaglandin D2 receptor

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

nanobody Nb35

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Cartoon
Tube
Trace
Lines
Ball+Stick
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Surface
Spacefill
Outline
Fog

Background

Transparent

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Extreme

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