SMTL ID : 7awd.1

Crystal structure of Peroxisome proliferator-activated receptor gamma (PPARG)in complex with garcinoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

2 x NQD: (2Z,6E,10E)-13-[(2R)-6-hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2,6,10-trimethyltrideca-2,6,10-trienoic acid(Non-covalent)

NQD.1: 21 residues within 4Å: Chain A: P.27, L.28, F.82, C.85, Q.86, R.88, S.89, A.92, E.95, H.123, I.126, Y.127, M.129, L.130, E.143, F.163, M.164, H.249, L.269, Y.273 Ligands: NQD.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.28, A:F.82, A:Q.86, A:R.88, A:A.92, A:I.126, A:Y.127, A:L.130, A:F.163, A:F.163 Hydrogen bonds: A:L.28, A:Q.86, A:S.89, A:E.143, A:Y.273 Water bridges: A:R.88 Salt bridges: A:H.123, A:H.249 NQD.2: 16 residues within 4Å: Chain A: I.49, E.59, I.62, K.63, F.64, Q.73, R.80, I.81, C.85, R.88, L.133, L.140, I.141, S.142, E.143 Ligands: NQD.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.49, A:E.59, A:I.62, A:R.80, A:I.81, A:L.133, A:I.141, A:I.141 Hydrogen bonds: A:E.59, A:F.64, A:S.142, A:E.143 Salt bridges: A:R.88

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 5 residues within 4Å: Chain A: L.118, K.119, L.268, E.271, I.272 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.268

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.34, N.135, K.136 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.34, A:K.136, A:K.136 Water bridges: A:N.135, A:N.135, A:K.136 GOL.5: 4 residues within 4Å: Chain A: K.136, D.137, R.150, E.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.136, A:D.137, A:D.137 Water bridges: A:E.151 GOL.6: 3 residues within 4Å: Chain A: N.135, D.137, F.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.135, A:D.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Willems, S. et al., Endogenous vitamin E metabolites mediate allosteric PPAR gamma activation with unprecedented co-regulatory interactions. Cell Chem Biol (2021)

Release Date

2020-11-25

Peptides

Peroxisome proliferator-activated receptor gamma: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peroxisome proliferator-activated receptor gamma

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