SMTL ID : 7a77.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: N.86, E.87, R.206, G.209, L.210 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.86, A:E.87, A:E.87, A:E.87 Water bridges: A:N.86, A:N.86 EDO.4: 4 residues within 4Å: Chain A: R.114, D.127, L.130, T.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.102, A:R.114, A:D.127, A:T.131 EDO.5: 6 residues within 4Å: Chain A: M.140, Q.141, Y.188, E.190, Q.191, R.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.140, A:Q.191, A:R.194 Water bridges: A:Q.141 EDO.6: 4 residues within 4Å: Chain A: R.128, S.207, K.211 Chain C: L.210 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.128, A:S.207, A:S.207, A:K.211 EDO.7: 5 residues within 4Å: Chain C: N.86, E.87, R.206, G.209, L.210 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.86, C:E.87, C:E.87 Water bridges: C:N.86, C:N.86 EDO.10: 4 residues within 4Å: Chain C: R.114, D.127, L.130, T.131 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.114, C:D.127 EDO.11: 6 residues within 4Å: Chain C: M.140, Q.141, Y.188, E.190, Q.191, R.194 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:M.140, C:Q.191, C:R.194 Water bridges: C:Q.141 EDO.12: 4 residues within 4Å: Chain A: L.210 Chain C: R.128, S.207, K.211 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.128 Water bridges: C:S.207, C:S.207, C:K.211

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 15 residues within 4Å: Chain A: I.48, A.51, A.52, Q.55, N.86, F.93, R.96, L.106, A.107, I.125, F.126, C.212, H.215, L.216, F.219 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.52, A:Q.55, A:F.93, A:F.93, A:F.93, A:I.125, A:F.126, A:H.215, A:L.216, A:L.216, A:F.219 Hydrogen bonds: A:A.107 Water bridges: A:Q.55, A:F.93 Salt bridges: A:R.96 PLM.8: 15 residues within 4Å: Chain C: I.48, A.51, A.52, Q.55, N.86, F.93, R.96, L.106, A.107, I.125, F.126, C.212, H.215, L.216, F.219 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.52, C:Q.55, C:F.93, C:F.93, C:F.93, C:I.125, C:F.126, C:H.215, C:L.216, C:L.216, C:F.219 Hydrogen bonds: C:A.107 Water bridges: C:Q.55, C:F.93 Salt bridges: C:R.96

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

CL.3: 3 residues within 4Å: Chain A: R.173 Chain C: L.200, R.201 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: L.200, R.201 Chain C: R.173 Ligand excluded by PLIP

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-alpha: 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-alpha

Nuclear receptor coactivator 2

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