ISDA

Entry Detail

PDB ID:

3W0J

Keywords:

TRANSCRIPTION

Title:

Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands

Biological Source:

Source Organism:

Rattus norvegicus, Homo sapiens

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2012-10-30

Release Date:

2013-10-09

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.84 Å

R-Value Free:

0.25

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Vitamin D3 Receptor
Chain IDs:A
Chain Length:253
Number of Molecules:1
Biological Source:Rattus norvegicus

UniProt ID:P13053 Pfam ID:PF00104

Protein Blast

Polymer Type:polypeptide(L)
Description:Mediator of RNA polymerase II transcription subunit 1
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15648

Ligand Molecules

T08

Primary Citation

Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands.

Asano, L, Ito, I, Kuwabara, N, Waku, T, Yanagisawa, J, Miyachi, H, Shimizu, T.Show

Febs Lett. 587 957 963 (2013)

PMID: 23462137 DOI: 10.1016/j.febslet.2013.02.028

Abstact

Non-secosteroidal ligands for vitamin D receptor (VDR) have been developed for the agonist with non-calcemic profiles. Here, we provide the structural mechanism of VDR agonism by novel non-secosteroidal ligands. All ligands had the similar efficacy, while two had the higher potency. Crystallographic analyses revealed that all ligands interacted with helix H10 and the loop between helices H6 and H7 in a similar manner, but also that the two ligands with higher potency had different interaction modes. This study suggests that distinct ligand potency depend upon differences in the formation and rearrangement of hydrogen-bond networks induced by each ligand.

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Primary Citation of related structures