SMTL ID : 4em9.3 (2 other biounits)

Human PPAR gamma in complex with nonanoic acids

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

8 x KNA: nonanoic acid(Non-covalent)

KNA.1: 13 residues within 4Å: Chain A: C.83, R.86, S.87, A.90, I.124, Y.125, L.128, L.131, F.161, M.162, K.165, H.247 Ligands: GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.86, A:A.90, A:Y.125, A:L.128, A:F.161 Hydrogen bonds: A:I.124 Salt bridges: A:R.86 KNA.5: 13 residues within 4Å: Chain B: C.83, R.86, S.87, A.90, I.124, Y.125, L.128, L.131, F.161, M.162, K.165, H.247 Ligands: GOL.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.86, B:A.90, B:Y.125, B:L.128, B:F.161 Hydrogen bonds: B:I.124 Salt bridges: B:R.86 KNA.9: 10 residues within 4Å: Chain C: C.83, R.86, S.87, A.90, I.124, L.128, L.131, M.162 Ligands: KNA.11, GOL.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.86, C:A.90 Salt bridges: C:R.86 KNA.10: 10 residues within 4Å: Chain C: F.80, C.83, S.87, H.121, L.154, F.158, F.161, H.247, L.251, Y.271 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.80, C:L.154, C:F.161 Hydrogen bonds: C:S.87, C:Y.271 Salt bridges: C:H.121, C:H.247 KNA.11: 7 residues within 4Å: Chain C: R.86, L.128, L.131, L.138, I.139, S.140 Ligands: KNA.9 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.86, C:I.139 Water bridges: C:R.86, C:E.141 KNA.13: 10 residues within 4Å: Chain D: C.83, R.86, S.87, A.90, I.124, L.128, L.131, M.162 Ligands: KNA.15, GOL.16 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:R.86, D:A.90 Salt bridges: D:R.86 KNA.14: 10 residues within 4Å: Chain D: F.80, C.83, S.87, H.121, L.154, F.158, F.161, H.247, L.251, Y.271 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.80, D:L.154, D:F.161 Hydrogen bonds: D:S.87 Salt bridges: D:H.121, D:H.247 KNA.15: 7 residues within 4Å: Chain D: R.86, L.128, L.131, L.138, I.139, S.140 Ligands: KNA.13 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:R.86, D:I.139 Water bridges: D:R.86, D:E.141

2 x TCE: 3,3',3''-phosphanetriyltripropanoic acid(Non-covalent)

TCE.2: 12 residues within 4Å: Chain A: L.53, E.57, F.62, H.64, I.79, G.82, C.83, R.86, I.139, S.140, M.146, F.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.79, A:S.140 Salt bridges: A:H.64 TCE.6: 12 residues within 4Å: Chain B: L.53, E.57, F.62, H.64, I.79, G.82, C.83, R.86, I.139, S.140, M.146, F.161 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.57, B:I.79, B:S.140 Salt bridges: B:H.64

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: N.110 Chain D: K.38, S.43 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.110, A:N.110, D:K.38 GOL.4: 9 residues within 4Å: Chain A: F.24, P.25, L.26, R.86, E.93, M.127, S.130, L.131 Ligands: KNA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.26, A:R.86, A:E.93, A:M.127 Water bridges: A:S.130 GOL.7: 3 residues within 4Å: Chain B: N.110 Chain C: K.38, S.43 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.38, B:N.110, B:N.110 GOL.8: 9 residues within 4Å: Chain B: F.24, P.25, L.26, R.86, E.93, M.127, S.130, L.131 Ligands: KNA.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.26, B:R.86, B:E.93, B:M.127 Water bridges: B:S.130 GOL.12: 9 residues within 4Å: Chain C: F.24, P.25, L.26, R.86, E.93, M.127, S.130, L.131 Ligands: KNA.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.26, C:R.86, C:E.93 Water bridges: C:S.130 GOL.16: 9 residues within 4Å: Chain D: F.24, P.25, L.26, R.86, E.93, M.127, S.130, L.131 Ligands: KNA.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.26, D:R.86, D:E.93 Water bridges: D:S.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liberato, M.V. et al., Medium chain fatty acids are selective peroxisome proliferator activated receptor (PPAR) Gamma activators and pan-PPAR partial agonists. Plos One (2012)

Release Date

2013-03-06

Peptides

Peroxisome proliferator-activated receptor gamma: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

Peroxisome proliferator-activated receptor gamma

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