SMTL ID : 6jey.1

Covalent bond formation between ynone moiety of synthetic fatty acid and hPPARg-LBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

3 x EJL: (9Z,12Z,15Z,18Z,21Z)-5-oxidanylidenetetracosa-9,12,15,18,21-pentaen-6-ynoic acid(Non-covalent)(Covalent)

EJL.1: 16 residues within 4Å: Chain A: F.25, P.26, L.27, C.84, R.87, S.88, E.94, I.125, Y.126, M.128, L.129, L.132, I.140, S.141, E.142 Ligands: EJL.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.25, A:F.25, A:L.27, A:L.27, A:R.87, A:I.125, A:M.128, A:L.129, A:L.132, A:I.140 Hydrogen bonds: A:R.87 EJL.2: 19 residues within 4Å: Chain A: I.80, F.81, G.83, C.84, Q.85, R.87, S.88, V.138, L.139, I.140, M.147, L.152, F.162, M.163, K.166, H.248, L.252, Y.272 Ligands: EJL.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.80, A:R.87, A:V.138, A:V.138, A:I.140, A:I.140, A:L.152, A:L.152 Hydrogen bonds: A:K.166, A:Y.272, A:Y.272 Salt bridges: A:H.248 EJL.3: 12 residues within 4Å: Chain B: G.83, C.84, F.86, R.87, E.90, I.125, L.129, L.132, L.139, I.140, S.141, E.142 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.86, B:F.86, B:R.87, B:R.87, B:R.87, B:L.129, B:I.140, B:I.140, B:E.142 Hydrogen bonds: B:I.125 Salt bridges: B:R.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kojima, H. et al., Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins. Cell Chem Biol (2020)

Release Date

2020-02-12

Peptides

Peroxisome proliferator-activated receptor gamma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peroxisome proliferator-activated receptor gamma

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