SMTL ID : 5v39.1

Crystal structure of human vitamin D receptor ligand binding domain in complex with a VDRM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 8VM: 5-(3-{4-[(2S)-2-hydroxy-3,3-dimethylbutoxy]-3-methylphenyl}pentan-3-yl)-3-methyl-N-(1H-tetrazol-5-yl)thiophene-2-carboxamide(Non-covalent)

8VM.1: 24 residues within 4Å: Chain A: Y.25, F.32, L.58, L.61, A.62, L.64, V.65, Y.67, S.68, I.102, R.105, S.106, S.109, W.117, C.119, Y.126, V.131, H.136, L.140, L.144, H.228, L.235, V.249, F.253 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.58, A:L.61, A:A.62, A:L.64, A:V.65, A:W.117, A:W.117, A:W.117, A:W.117, A:Y.126, A:V.131, A:V.131, A:L.140, A:L.144, A:L.235, A:V.249, A:F.253 Hydrogen bonds: A:Y.25, A:S.68, A:S.68, A:R.105 Water bridges: A:D.26, A:S.106, A:S.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, J. et al., HDX reveals the conformational dynamics of DNA sequence specific VDR co-activator interactions. Nat Commun (2017)

Release Date

2018-03-14

Peptides

Vitamin D3 receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vitamin D3 receptor