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SMTL ID : 9e9s.1

Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.68 Å

Oligo State

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

Ligands

1 x PG2: PROSTAGLANDIN D2(Non-covalent)

PG2.1:

18 residues within 4Å:

Chain D: G.49, L.52, F.53, G.101, K.102, L.105, S.106, V.109, Y.113, M.138, T.207, W.208, L.332, L.335, R.336, L.338, S.339, S.342

12 PLIP interactions:

12 interactions with chain D

Hydrophobic interactions: D:L.105, D:V.109, D:V.109, D:L.332, D:L.335, D:L.338
Hydrogen bonds: D:K.102, D:K.102, D:S.106, D:Y.113, D:S.342
Salt bridges: D:R.336

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2:

5 residues within 4Å:

Chain D: P.30, Y.32, R.33, Q.35, N.36

3 PLIP interactions:

3 interactions with chain D

Hydrophobic interactions: D:P.30
Hydrogen bonds: D:Q.35, D:N.36

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3:

13 residues within 4Å:

Chain D: M.89, C.92, G.93, V.96, T.97, L.100, L.104, F.137, F.140, A.176, A.179, P.180, S.183

10 PLIP interactions:

10 interactions with chain D

Hydrophobic interactions: D:V.96, D:L.100, D:L.104, D:L.104, D:F.137, D:F.137, D:F.140, D:A.179
Hydrogen bonds: D:M.89
Water bridges: D:A.179

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Davoudinasab, B. et al., Cryo-EM structure of inactive and active prostaglandin D2 receptor. To Be Published

Release Date

2025-09-03

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
Prostaglandin D2 receptor: D
Nanobody35|Lama glama: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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

Prostaglandin D2 receptor

Nanobody35|Lama glama

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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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