SMTL ID : 7m8w.1

XFEL crystal structure of the prostaglandin D2 receptor CRTH2 in complex with 15R-methyl-PGD2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

monomer

Ligands

1 x YSS: 15R-methyl-prostaglandin D2(Non-covalent)

YSS.1: 17 residues within 4Å: Chain A: F.88, F.91, W.98, H.108, F.112, F.113, R.171, M.182, C.183, Y.184, Y.185, K.211, Y.387, L.411, P.412, T.415, F.419 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.88, A:F.91, A:W.98, A:F.112, A:F.112, A:F.113, A:Y.184, A:Y.387, A:L.411, A:P.412, A:T.415, A:F.419 Hydrogen bonds: A:R.171, A:C.183, A:C.183, A:Y.185, A:Y.387 Water bridges: A:K.211 Salt bridges: A:R.171, A:K.211

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: L.74, S.77, D.78, N.115, S.119, N.425 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.77, A:S.119, A:N.425 Water bridges: A:N.115

1 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 7 residues within 4Å: Chain A: T.65, V.66, V.67, Q.133, R.144, R.368, F.369 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.65, A:V.66, A:V.67 Water bridges: A:R.349 Salt bridges: A:R.144, A:R.144, A:R.368

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 7 residues within 4Å: Chain A: R.144, T.145, V.146, T.343, P.344, N.345, R.346 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.145, A:V.146, A:A.147, A:N.345, A:N.345, A:R.346 SO4.5: 3 residues within 4Å: Chain A: R.320, Q.324, R.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.324, A:Q.324 Salt bridges: A:R.320, A:R.326 SO4.6: 4 residues within 4Å: Chain A: Q.141, W.359, Y.362, R.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.141, A:Q.141 Salt bridges: A:R.364 SO4.7: 6 residues within 4Å: Chain A: G.314, F.315, T.316, N.317, S.318, N.333 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.315, A:T.316, A:N.317, A:S.318, A:S.318, A:N.333 SO4.8: 3 residues within 4Å: Chain A: R.363, R.364, R.365 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.363, A:R.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Molecular basis for lipid recognition by the prostaglandin D 2 receptor CRTH2. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-08-25

Peptides

Prostaglandin D2 receptor 2, Endolysin chimera: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Prostaglandin D2 receptor 2, Endolysin chimera

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