SMTL ID : 3a40.1

Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277B(C23R)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x 23R: (1S,2S,3R,5Z,7E,14beta,17alpha,23R)-23-(2-hydroxy-2-methylpropyl)-2-methyl-20,24-epoxy-9,10-secochola-5,7,10-triene-1,3-diol(Non-covalent)

23R.1: 19 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, H.233 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.30, A:F.37, A:L.63, A:L.66, A:L.69, A:L.69, A:I.107, A:W.122, A:Y.131, A:V.136, A:L.145 Hydrogen bonds: A:Y.30, A:S.73, A:R.110, A:S.114, A:H.233

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

SO4.2: 5 residues within 4Å: Chain A: Q.243, P.244, E.245, C.246, S.247 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.243, A:E.245, A:C.246, A:S.247, A:S.247, A:S.247 Water bridges: A:M.248 SO4.3: 4 residues within 4Å: Chain A: F.115, T.116, M.117, K.157 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.117 Water bridges: A:N.112, A:F.115, A:K.157, A:K.157 Salt bridges: A:K.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antony, P. et al., Structure-function relationships and crystal structures of the vitamin D receptor bound 2 alpha-methyl-(20S,23S)- and 2 alpha-methyl-(20S,23R)-epoxymethano-1 alpha,25-dihydroxyvitamin D3. J.Med.Chem. (2010)

Release Date

2010-02-02

Peptides

Vitamin D3 receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

Vitamin D3 receptor

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