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SMTL ID : 9au0.1

Cryo-EM structure of the BW245C-bound prostaglandin D2 receptor (DP1)-Gs complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.45 Å

Oligo State

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

Ligands

1 x 01: 7-{(4S)-3-[(3R)-3-cyclohexyl-3-hydroxypropyl]-2,5-dioxoimidazolidin-4-yl}heptanoic acid

01.1:

15 residues within 4Å:

Chain E: G.49, L.52, F.53, K.102, S.106, V.109, Y.113, M.138, G.142, T.207, W.208, R.336, L.338, S.339, S.342

8 PLIP interactions:

8 interactions with chain E

Hydrophobic interactions: E:V.109, E:L.338
Hydrogen bonds: E:G.49, E:K.102, E:S.106, E:T.207, E:S.342
Salt bridges: E:R.336

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

NAG.2:

5 residues within 4Å:

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

2 PLIP interactions:

2 interactions with chain E

Hydrogen bonds: E:Q.35, E:Q.35

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3:

10 residues within 4Å:

Chain E: M.89, V.96, T.97, L.100, L.104, F.137, F.140, A.176, A.179, S.183

9 PLIP interactions:

9 interactions with chain E

Hydrophobic interactions: E:V.96, E:L.100, E:L.104, E:L.104, E:F.137, E:F.137, E:F.140, E:A.179
Hydrogen bonds: E:A.176

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

2025-08-27

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
Nanobody-35: D
Prostaglandin D2 receptor: 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

Nanobody-35

Prostaglandin D2 receptor

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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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