5B41: VDR-LBD

Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3. Determined by X-ray diffraction at 1.89 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 1.89 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 2
Atoms: 2,182
Mol. weight: 32.58 kDa
Ligands: YSV
Released: 7 Dec 2016

Explore 5B41 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B41 contains 14 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: 13 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	223-242	20
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	303-319	17
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	628-634	7

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>5B41_1 Vitamin D3 receptor (chains A)
GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGS
VTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSN
QSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEE
HSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Sequence of entity 2 (C), FASTA

>5B41_2 Mediator of RNA polymerase II transcription subunit 1 (chains C)
KNHPMLMNLLKDN

Ligands and cofactors

ID	Name	Formula	Copies
YSV	(1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloct…	C27 H44 O3	1

Primary citation

Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics. Anami, Y., Shimizu, N., Ekimoto, T. et al. J Med Chem (2016) 59:7888-7900. DOI 10.1021/acs.jmedchem.6b00682 · 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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