SMTL ID : 5u3s.1 (1 other biounit)

Human PPARdelta ligand-binding domain in complexed with specific agonist 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 7V4: 6-[2-({[4-(furan-3-yl)benzene-1-carbonyl](propan-2-yl)amino}methyl)phenoxy]hexanoic acid(Non-covalent)

7V4.1: 30 residues within 4Å: Chain A: I.44, L.50, W.59, V.76, F.77, R.79, C.80, Q.81, T.83, T.84, T.87, H.118, I.121, F.122, L.125, I.128, L.134, V.136, V.143, F.147, L.148, I.158, I.159, K.162, F.163, H.244, M.248, L.264, Y.268 Ligands: PGO.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:R.79, A:T.83, A:I.121, A:L.125, A:L.134, A:V.136, A:I.159, A:I.159, A:K.162, A:L.264 Hydrogen bonds: A:T.84, A:Y.268 Salt bridges: A:H.118, A:H.244

1 x B7G: heptyl beta-D-glucopyranoside(Non-covalent)

B7G.2: 10 residues within 4Å: Chain A: V.88, T.92, V.110, L.113, K.114, L.263, E.266, I.267, K.269, D.270 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.113, A:L.113, A:E.266, A:I.267 Hydrogen bonds: A:K.114, A:E.266, A:K.269 Salt bridges: A:K.114

3 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.3: 7 residues within 4Å: Chain A: T.83, T.87, I.121, M.124, L.125, I.128 Ligands: 7V4.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.90 PGO.4: 9 residues within 4Å: Chain A: I.31, L.32, G.34, A.40, P.41, V.43, N.130, L.135, F.142 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.41, A:V.43, A:F.142 Hydrogen bonds: A:L.32 Water bridges: A:N.130 PGO.6: 10 residues within 4Å: Chain A: Q.61, L.66, P.67, Y.78, Q.81, C.82, S.259, L.260, H.261, P.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.81

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 7 residues within 4Å: Chain A: D.191, Q.205, L.209, L.231, M.234, A.235, R.238 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.7: 6 residues within 4Å: Chain A: R.29, V.129, N.130, K.131, V.167, N.170 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, C.C. et al., Structural basis for specific ligation of the peroxisome proliferator-activated receptor delta. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-03-22

Peptides

Peroxisome proliferator-activated receptor delta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peroxisome proliferator-activated receptor delta

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