3AUN: Rat vitamin D receptor ligand binding domain

Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR335 and a synthetic peptide containing the NR2 box of DRIP 205. Determined by X-ray diffraction at 1.81 Å resolution. Released 15 Feb 2012.

Method: X-ray diffraction
Resolution: 1.81 Å
Organisms: Rattus norvegicus, synthetic construct
Chains: 2
Atoms: 2,181
Mol. weight: 32.1 kDa
Ligands: YR4
Released: 15 Feb 2012

Explore 3AUN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3AUN contains 16 α-helices and 3 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	126-142	17
α-helix	148-152	5
α-helix	154-156	3
α-helix	223-241	19
α-helix	247-249	3
α-helix	252-270	19
α-helix	271-273	3
β-strand	275-276	2	1
β-strand	281-283	3	1
β-strand	290-291	2	1
α-helix	293-297	5
α-helix	303-317	15
α-helix	323-334	12
α-helix	345-366	22
α-helix	367-368	2
α-helix	375-401	27
α-helix	404-407	4
α-helix	412-418	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	629-634	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin D3 receptor	A	protein	265	Rattus norvegicus	P13053 (AlphaFold model)
DRIP 205 NR2 box peptide	B	protein	13	synthetic construct	Q15648 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3AUN_1 Vitamin D3 receptor (chains A)
GSHMLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGSVTLDLS
PLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMD
DMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPD
RPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYR
SLSFQPENSMKLTPLVLEVFGNEIS

Sequence of entity 2 (B), FASTA

>3AUN_2 DRIP 205 NR2 box peptide (chains B)
KNHPMLMNLLKDN

Ligands and cofactors

ID	Name	Formula	Copies
YR4	(2R)-2-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3…	C29 H44 O5	1

Primary citation

Design, synthesis and X-ray crystallographic study of new nonsecosteroidal vitamin D receptor ligands. Demizu, Y., Takahashi, T., Kaneko, F. et al. Bioorg Med Chem Lett (2011) 21:6104-6107. DOI 10.1016/j.bmcl.2011.08.047 · PubMed

Other PDB entries of the same protein (UniProt P13053 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9VOG 1.43 Å, Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid…
9M1D 1.44 Å, Vitamin D receptor complex with a methyldiphenylpropylsilane derivative
3VTC 1.5 Å, Crystal structure of rat vitamin D receptor bound to a partial agonist…
3VT7 1.65 Å, Crystal structures of rat VDR-LBD with W282R mutation
9M1C 1.67 Å, Vitamin D receptor complex with a triphenylpropylsilane derivative
9M13 1.68 Å, Vitamin D receptor complex with a dimethyldiphenylsilane derivative
2ZMI 1.7 Å, Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs:…
3VT3 1.7 Å, Crystal structures of rat VDR-LBD with R270L mutation
2O4J 1.74 Å, Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII…
9VOL 1.75 Å, Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)-2-methylphenoxy}butanoic acid…
9M1B 1.77 Å, Vitamin D receptor complex with a diphenydipropylsilane derivative
9M1A 1.78 Å, Vitamin D receptor complex with a diethyldiphenylsilane derivative

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