SMTL ID : 9ee5.1

Cryo-EM structure of the ONO2550289-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.89 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 01: [2-chloro-5-(2,6-dimethyl-4-{[(2S)-4-methyl-3,4-dihydro-2H-1,4-benzoxazin-2-yl]methoxy}benzamido)phenyl]acetic acid

01.1: 17 residues within 4Å: Chain D: N.44, M.48, G.49, D.98, G.101, K.102, L.105, S.106, M.138, F.141, W.208, R.425, L.427, S.428, I.430, S.431, I.432 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:K.102, D:L.105, D:F.141, D:W.208, D:I.430, D:I.432 Hydrogen bonds: D:N.44, D:S.428, D:S.428, D:S.431 Salt bridges: D:R.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davoudinasab, B. et al., Structural insights into mechanism of activation and deactivation of prostaglandin receptors. To Be Published

Release Date

2025-09-03

Peptides

anti-BRIL Fab Heavy Chain: A
anti-Fab Nanobody synthetic construct: B
anti-BRIL Fab Light Chain: C
Prostaglandin D2 receptor,Soluble cytochrome b562: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
K

C
L

D
A

Membrane

We predict this structure to be a membrane protein.
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anti-BRIL Fab Heavy Chain

anti-Fab Nanobody synthetic construct

anti-BRIL Fab Light Chain

Prostaglandin D2 receptor,Soluble cytochrome b562

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