SMTL ID : 7a78.1

Crystal structure of RXR beta LBD in complexes with palmitic acid and GRIP-1 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 16 residues within 4Å: Chain A: I.44, A.47, A.48, Q.51, N.82, F.89, R.92, L.102, A.103, V.118, I.121, F.122, C.208, H.211, L.212, F.215 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.48, A:Q.51, A:F.89, A:F.89, A:F.89, A:V.118, A:I.121, A:F.122, A:H.211, A:L.212, A:L.212, A:F.215 Hydrogen bonds: A:A.103 Water bridges: A:R.92 Salt bridges: A:R.92 PLM.8: 16 residues within 4Å: Chain C: I.44, A.47, A.48, Q.51, N.82, F.89, R.92, L.102, A.103, V.118, I.121, F.122, C.208, H.211, L.212, F.215 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.48, C:Q.51, C:F.89, C:F.89, C:F.89, C:V.118, C:I.121, C:F.122, C:H.211, C:L.212, C:L.212, C:F.215 Hydrogen bonds: C:A.103 Water bridges: C:R.92 Salt bridges: C:R.92

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: R.169 Chain C: L.196, R.197 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: L.196, R.197 Chain C: R.169 Ligand excluded by PLIP

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

EDO.3: 5 residues within 4Å: Chain A: M.4, P.5, V.6, S.175 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.6 Water bridges: A:S.175 EDO.4: 5 residues within 4Å: Chain A: M.4, K.171, A.174, S.175 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:S.175 EDO.5: 6 residues within 4Å: Chain A: R.78, A.79, G.80, W.81, N.82, L.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.82 Water bridges: A:E.83, A:E.83 EDO.6: 1 residues within 4Å: Chain A: H.114 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.114, A:H.114, A:H.114, A:H.114 EDO.7: 4 residues within 4Å: Chain A: Q.187, G.189, R.190, K.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.190 EDO.10: 5 residues within 4Å: Chain C: M.4, P.5, V.6, S.175 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.6 Water bridges: C:S.175 EDO.11: 5 residues within 4Å: Chain C: M.4, K.171, A.174, S.175 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.175, C:S.175 EDO.12: 6 residues within 4Å: Chain C: R.78, A.79, G.80, W.81, N.82, L.209 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.82 Water bridges: C:E.83 EDO.13: 1 residues within 4Å: Chain C: H.114 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.114 Water bridges: C:H.114 EDO.14: 4 residues within 4Å: Chain C: Q.187, G.189, R.190, K.193 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Comprehensive Set of Tertiary Complex Structures and Palmitic Acid Binding Provide Molecular Insights into Ligand Design for RXR Isoforms. Int J Mol Sci (2020)

Release Date

2020-10-21

Peptides

Retinoic acid receptor RXR-beta: AC
Nuclear receptor coactivator 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Retinoic acid receptor RXR-beta

Nuclear receptor coactivator 2

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