6D26: Prostaglandin D2 receptor CRTH2 with fevipiprant

Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant. Determined by X-ray diffraction at 2.8 Å resolution. Released 3 Oct 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 1
Atoms: 3,650
Mol. weight: 54.62 kDa
Ligands: FSY, SIN, OLA, PGO
Released: 3 Oct 2018

Explore 6D26 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D26 contains 30 α-helices and 2 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 30 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	33-55	23
α-helix	56-60	5
α-helix	65-93	29
α-helix	102-134	33
α-helix	136-142	7
α-helix	145-161	17
α-helix	164-168	5
β-strand	170-174	5	1
β-strand	180-184	5	1
α-helix	186-188	3
α-helix	195-211	17
α-helix	212-216	5
α-helix	217-1241	24
α-helix	1244-1246	3
α-helix	1254-1256	3
α-helix	1272-1281	10
α-helix	1286-1290	5
α-helix	1294-1307	14
α-helix	1309-1312	4
α-helix	1316-1323	8
α-helix	1327-1334	8
α-helix	1338-1342	5
α-helix	1344-1356	13
α-helix	2241-2242	2
α-helix	2245-2258	14
α-helix	2260-2271	12
α-helix	2276-2278	3
α-helix	2279-2282	4
α-helix	2286-2294	9
α-helix	2296-2307	12
α-helix	2309-2323	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin D2 receptor 2, Endolysin chimera	A	protein	470	Homo sapiens, Enterobacteria phage T4	P00720, Q9Y5Y4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6D26_1 Prostaglandin D2 receptor 2, Endolysin chimera (chains A)
GMSANATLKPLCPILEQMSRLQSHSATSIRYIDHAAVLLHGLASLLGLVENGVILFVVGC
RMRQTVVTTWVLHLALSDLLASASLPFFTYFLAVGHSWELGTTFCKLHSSIFFLNMFASG
FLLSAISLDRCLQVVRPVWAQNHRTVAAAHKVCLVLWALAVLNTVPYFVFRDTISRLDGR
IMCYYNVLLLNPGPDRDATCNSRQAALAVSKFLLAFLVPLAIIASSHAAVSLRLQHRADL
GLQHRNIFEMLRIDEGGGSGGDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL
INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWD
AYRRRPGRFVRLVAAVVAAFALCWGPYHVFSLLEARAHANPGLRPLVWRGLPFVTSLAFF
NSVANPVLYVLTCPDMLRKLRRSLRTVLESVLVDDSELGGAGSSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
FSY	fevipiprant	C19 H17 F3 N2 O4 S	1
SIN	Succinic acid	C4 H6 O4	5
OLA	Oleic acid	C18 H34 O2	1
PGO	S-1,2-propanediol	C3 H8 O2	1

Water and common crystallization additives (SO4, PGE) are not listed.

Primary citation

Structures of the Human PGD2Receptor CRTH2 Reveal Novel Mechanisms for Ligand Recognition. Wang, L., Yao, D., Deepak, R.N.V.K. et al. Mol Cell (2018) 72:48-59.e4. DOI 10.1016/j.molcel.2018.08.009 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

Browse structure collections

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