SMTL ID : 7qpp.1

High resolution structure of human VDR ligand binding domain in complex with calcitriol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x VDX: 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL(Non-covalent)

VDX.1: 30 residues within 4Å: Chain A: Y.30, Y.34, F.37, L.63, L.66, A.67, L.69, V.70, S.73, I.104, I.107, M.108, R.110, S.111, E.113, S.114, W.122, C.124, Y.131, V.136, A.139, H.141, L.145, L.149, H.233, Y.237, L.240, L.250, V.254, F.258 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.30, A:L.63, A:L.69, A:L.69, A:I.107, A:W.122, A:V.136, A:L.145, A:L.149, A:V.254 Hydrogen bonds: A:Y.30, A:S.73, A:R.110, A:S.114, A:S.114, A:H.141, A:H.233

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

SO4.2: 6 residues within 4Å: Chain A: Q.243, P.244, E.245, C.246, S.247, M.248 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.245, A:C.246, A:S.247, A:S.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sigueiro, R. et al., Advances in Vitamin D Receptor Function and Evolution Based on the 3D Structure of the Lamprey Ligand-Binding Domain. J.Med.Chem. (2022)

Release Date

2022-12-28

Peptides

Vitamin D3 receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vitamin D3 receptor

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