3VRV: VDR ligand binding domain

VDR ligand binding domain in complex with 2-Methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 May 2012.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 2
Atoms: 2,112
Mol. weight: 32.6 kDa
Ligands: YSD
Released: 23 May 2012

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

Secondary structure: helices and β-sheets

3VRV contains 15 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: 14 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	223-243	21
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	375-402	28
α-helix	404-407	4
α-helix	412-418	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	628-633	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin D3 receptor	A	protein	271	Rattus norvegicus	P13053 (AlphaFold model)
13-meric peptide from Mediator of RNA polymerase II transcription subunit 1	C	protein	13	Homo sapiens	Q15648 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VRV_1 Vitamin D3 receptor (chains A)
GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGS
VTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSN
QSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEE
HSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Sequence of entity 2 (C), FASTA

>3VRV_2 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (chains C)
KNHPMLMNLLKDN

Ligands and cofactors

ID	Name	Formula	Copies
YSD	(1R,3R,7E,17beta)-17-[(2R)-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-sec…	C28 H46 O3	1

Primary citation

Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands. Yoshimoto, N., Sakamaki, Y., Haeta, M. et al. J Med Chem (2012) 55:4373-4381. DOI 10.1021/jm300230a · 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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