2O4J: Rat Vitamin D Receptor Ligand Binding Domain

Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205. Determined by X-ray diffraction at 1.74 Å resolution. Released 30 Jan 2007.

Method: X-ray diffraction
Resolution: 1.74 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 2,242
Mol. weight: 34.97 kDa
Ligands: VD4
Released: 30 Jan 2007

Explore 2O4J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2O4J 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	223-243	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
α-helix	287-289	3
β-strand	290-291	2	1
α-helix	293-297	5
α-helix	303-318	16
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	292	Rattus norvegicus	P13053 (AlphaFold model)
Peroxisome proliferator-activated receptor-binding protein	C	protein	13		Q15648 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2O4J_1 Vitamin D3 receptor (chains A)
LKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGSVTLDLSPLSM
LPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW
DCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGV
QDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSF
QPENSMKLTPLVLEVFGNEISLVPRGSMAISDPNSSSVDKLAAALEHHHHHH

Sequence of entity 2 (C), FASTA

>2O4J_2 Peroxisome proliferator-activated receptor-binding protein (chains C)
KNHPMLMNLLKDN

Ligands and cofactors

ID	Name	Formula	Copies
VD4	(1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra…	C27 H42 O3	1

Primary citation

New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D(3) with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations. Vanhooke, J.L., Tadi, B.P., Benning, M.M. et al. Arch Biochem Biophys (2007) 460:161-165. DOI 10.1016/j.abb.2006.11.029 · 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
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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