SMTL ID : 5zqu.1

Crystal structure of tetrameric RXRalpha-LBD complexed with partial agonist CBt-PMN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

6 x 9HF: 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)benzotriazole-5-carboxylic acid(Non-covalent)

9HF.1: 14 residues within 4Å: Chain A: A.52, A.53, Q.56, L.57, W.86, N.87, L.90, F.94, R.97, L.107, A.108, T.109, F.219 Ligands: 9HF.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.56, A:L.57, A:W.86, A:L.90, A:F.219 Hydrogen bonds: A:Q.56, A:A.108, A:T.109 Salt bridges: A:R.97 pi-Stacking: A:F.219 9HF.2: 9 residues within 4Å: Chain A: A.53, W.86, L.214, F.219, F.220 Chain C: L.217, F.220 Ligands: 9HF.1, 9HF.11 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.53, A:L.214, A:F.219, A:F.220, C:L.217, C:F.220 pi-Stacking: A:F.220, C:F.220 9HF.7: 14 residues within 4Å: Chain B: I.49, A.52, A.53, Q.56, L.57, W.86, L.90, F.94, R.97, L.107, A.108, F.219, F.220, I.223 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.53, B:Q.56, B:L.57, B:W.86, B:L.90, B:F.219, B:F.219 Hydrogen bonds: B:A.108 Salt bridges: B:R.97 pi-Stacking: B:F.219 9HF.11: 13 residues within 4Å: Chain C: I.49, A.52, A.53, Q.56, W.86, L.90, R.97, L.107, A.108, F.219, F.220, I.223 Ligands: 9HF.2 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.53, C:Q.56, C:W.86, C:L.90, C:F.219, C:F.219, C:F.219 Hydrogen bonds: C:A.108, C:T.109 Salt bridges: C:R.97 pi-Stacking: C:F.219 9HF.14: 12 residues within 4Å: Chain D: A.53, Q.56, L.57, W.86, N.87, L.90, F.94, R.97, L.107, A.108, F.219 Ligands: 9HF.15 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.53, D:Q.56, D:L.57, D:W.86, D:L.90, D:F.219 Hydrogen bonds: D:A.108 Salt bridges: D:R.97 9HF.15: 9 residues within 4Å: Chain B: C.50, L.217, F.220 Chain D: A.53, W.86, L.214, F.219, F.220 Ligands: 9HF.14 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:A.53, D:L.214, D:F.219, D:F.220, B:L.217, B:F.220 pi-Stacking: D:F.220, B:F.220

11 x BR: BROMIDE ION(Non-covalent)

BR.3: 2 residues within 4Å: Chain A: R.174 Chain B: R.202 Ligand excluded by PLIP BR.4: 2 residues within 4Å: Chain A: R.202 Chain B: R.174 Ligand excluded by PLIP BR.5: 2 residues within 4Å: Chain A: I.126, R.129 Ligand excluded by PLIP BR.6: 3 residues within 4Å: Chain A: R.129, S.208 Chain B: R.207 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain B: W.63, G.149, R.152 Ligand excluded by PLIP BR.9: 3 residues within 4Å: Chain B: A.125, I.126, R.129 Ligand excluded by PLIP BR.10: 1 residues within 4Å: Chain B: R.152 Ligand excluded by PLIP BR.12: 2 residues within 4Å: Chain C: R.174 Chain D: R.202 Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain C: I.126, R.129, K.212 Ligand excluded by PLIP BR.16: 2 residues within 4Å: Chain C: R.202 Chain D: R.174 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain D: A.125, I.126, R.129 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyashita, Y. et al., Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor alpha (RXR alpha ). FEBS Lett. (2019)

Release Date

2019-02-27

Peptides

Retinoic acid receptor RXR-alpha: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Retinoic acid receptor RXR-alpha

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