SMTL ID : 5yt2.1

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 90O: (1R,2S,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol(Non-covalent)

90O.1: 21 residues within 4Å: Chain A: T.25, Y.26, D.27, Y.30, L.59, L.65, V.66, Y.68, S.69, K.72, I.100, R.106, S.107, S.110, W.118, C.120, V.132, H.137, L.141, L.145, H.229 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.26, A:Y.30, A:L.59, A:L.65, A:I.100, A:W.118, A:W.118, A:V.132, A:L.141, A:L.145 Hydrogen bonds: A:T.25, A:Y.26, A:D.27, A:S.69, A:R.106, A:R.106, A:S.110, A:H.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sawada, D. et al., Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor. Org. Biomol. Chem. (2018)

Release Date

2018-04-11

Peptides

Vitamin D3 receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vitamin D3 receptor

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