3VTC: Rat vitamin D receptor

Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK3. Determined by X-ray diffraction at 1.5 Å resolution. Released 12 Jun 2013.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 2,346
Mol. weight: 32.76 kDa
Ligands: TK3
Released: 12 Jun 2013

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

Secondary structure: helices and β-sheets

3VTC 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
α-helix	287-289	3
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	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	628-634	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin D3 receptor	A	protein	271	Rattus norvegicus	P13053 (AlphaFold model)
Coactivator peptide drip	B	protein	13

Sequence of entity 1 (A), FASTA

>3VTC_1 Vitamin D3 receptor (chains A)
GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGS
VTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSN
QSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEE
HSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Sequence of entity 2 (B), FASTA

>3VTC_2 COACTIVATOR PEPTIDE DRIP (chains B)
KNHPMLMNLLKDN

Ligands and cofactors

ID	Name	Formula	Copies
TK3	(1R,3R,7E,17beta)-17-{(2R,6R)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec…	C36 H52 O3	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor. Kudo, T., Ishizawa, M., Maekawa, K. et al. J Med Chem (2014). DOI 10.1021/jm401989c · 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
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
3W0H 1.8 Å, Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel…

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