SMTL ID : 7qpi.1

Structure of lamprey VDR in complex with 1,25D3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

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: 17 residues within 4Å: Chain A: Y.27, Y.31, L.87, V.94, S.97, I.131, R.134, S.135, S.138, W.146, C.148, Y.155, V.160, H.165, H.257, Y.261, L.278 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.87, A:I.131, A:W.146, A:Y.155, A:V.160, A:V.160, A:L.278 Hydrogen bonds: A:Y.27, A:S.97, A:R.134, A:S.138, A:H.165

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.231, P.232, L.233 No protein-ligand interaction detected (PLIP) MG.3: 6 residues within 4Å: Chain A: T.26, Y.27, D.28, Y.96, K.100, R.134 No protein-ligand interaction detected (PLIP)

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

2022-12-14

Peptides

Vitamin D receptor: A
Nuclear receptor coactivator 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
U

Vitamin D receptor

Nuclear receptor coactivator 1

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