SMTL ID : 3a78.1

Crystal structure of the human VDR ligand binding domain bound to the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 3EV: (1S,3S,5Z,7E,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-1,3,25-triol(Non-covalent)

3EV.1: 20 residues within 4Å: Chain A: Y.30, Y.34, F.37, L.63, L.66, L.69, V.70, S.73, I.107, R.110, S.111, S.114, W.122, C.124, Y.131, V.136, H.141, L.145, L.149, H.233 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.30, A:L.63, A:L.66, A:L.69, A:W.122, A:Y.131, A:V.136, A:V.136, A:L.145, A:L.149 Hydrogen bonds: A:Y.30, A:S.73, A:R.110, A:S.114, A:H.141

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: P.244, E.245, C.246, S.247 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.245, A:C.246, A:S.247, A:S.247, A:S.247 SO4.3: 4 residues within 4Å: Chain A: F.115, T.116, M.117, K.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.117 Water bridges: A:K.157 Salt bridges: A:K.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Molnar, F. et al., Structural basis of the activation of the human Vitamin D receptor by the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3. To be Published

Release Date

2010-10-13

Peptides

Vitamin D3 receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vitamin D3 receptor

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