SMTL ID : 3vrt.1

VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x YS2: (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol(Non-covalent)

YS2.1: 17 residues within 4Å: Chain A: Y.38, Y.42, F.45, L.77, V.78, S.81, I.112, I.115, R.118, S.119, S.122, W.130, C.132, V.144, H.149, L.157, H.241 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.38, A:F.45, A:L.77, A:I.112, A:I.115, A:W.130, A:W.130, A:W.130, A:V.144, A:L.157 Hydrogen bonds: A:S.81, A:R.118, A:S.122, A:S.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshimoto, N. et al., Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands. J.Med.Chem. (2012)

Release Date

2012-05-23

Peptides

Vitamin D3 receptor: A
13-meric peptide from Mediator of RNA polymerase II transcription subunit 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Vitamin D3 receptor

13-meric peptide from Mediator of RNA polymerase II transcription subunit 1

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