SMTL ID : 8fkg.1

Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR33486

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: K.14 Chain B: Q.93 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.93, A:K.14 GOL.3: 5 residues within 4Å: Chain B: M.51, R.156, S.263, L.264, H.265 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.156, B:R.156, B:S.263, B:H.265

1 x Y62: 2-chloro-N-(5-cyanopyridin-2-yl)-5-nitrobenzamide

Y62.2: 15 residues within 4Å: Chain B: I.80, F.81, C.84, Q.85, H.122, Y.126, F.162, M.163, K.166, V.245, H.248, Y.272, L.275, Y.276 Ligands: EDO.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.80, B:F.81, B:F.81, B:H.248, B:Y.276 Hydrogen bonds: B:Q.85, B:Y.276 pi-Stacking: B:H.248

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

SO4.4: 4 residues within 4Å: Chain B: R.33, N.134, K.135 Ligands: K.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.33, B:K.135 Water bridges: B:M.133, B:N.134

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain B: L.27, T.28, K.29, M.128, S.131, L.132 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.131 Water bridges: B:Y.21 EDO.6: 6 residues within 4Å: Chain B: F.162, K.166, E.247, H.248, L.251 Ligands: Y62.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.166, B:H.248 EDO.7: 3 residues within 4Å: Chain B: N.134, D.136, F.146 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.134, B:N.134, B:D.136 EDO.8: 4 residues within 4Å: Chain B: Y.119, R.196, P.197, R.242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.196 EDO.9: 4 residues within 4Å: Chain B: R.11, S.181, Q.219, N.223 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.181, B:S.181, B:Q.219 Water bridges: B:R.11 EDO.10: 4 residues within 4Å: Chain B: L.200, N.201, V.202, K.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.200, B:V.202, B:K.203 EDO.11: 7 residues within 4Å: Chain B: L.27, L.132, L.139, I.140, S.141, E.142, G.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.140, B:E.142, B:G.143 EDO.12: 3 residues within 4Å: Chain B: G.83, R.87, K.273 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.87, B:R.87, B:K.273

1 x K: POTASSIUM ION(Non-covalent)

K.13: 3 residues within 4Å: Chain B: K.135, D.136 Ligands: SO4.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

MacTavish, B.S. et al., Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and SR33486. To Be Published

Release Date

2024-04-17

Peptides

Nuclear receptor corepressor 1: A
Peroxisome proliferator-activated receptor gamma: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

Nuclear receptor corepressor 1

Peroxisome proliferator-activated receptor gamma

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