PDB 3vt5 biological assemblies and structure analysis ‹ Protein Data Bank in Europe (PDBe)

Assemblies

Assembly 1 (preferred)

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Assembly Name: Vitamin D3 receptor and peptide
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Multimeric state: hetero dimer

Accessible surface area: 11860.55 Å²

Buried surface area: 1088.23 Å²

Dissociation area: 544.12 Å²

Dissociation energy (ΔG^diss): 3.24 kcal/mol

Dissociation entropy (TΔS^diss): 7.5 kcal/mol

Symmetry number: 1

PDBe Complex ID: PDB-CPX-146455

$Hetero dimeric assembly 1 of PDB entry 3vt5 coloured by chemically distinct molecules, front view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Vitamin D3 receptor;</li> <li class='image_legend_li'>1 copy of COACTIVATOR PEPTIDE DRIP;</li> <li class='image_legend_li'>1 copy of (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Hetero dimeric assembly 1 of PDB entry 3vt5 coloured by chemically distinct molecules, side view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Vitamin D3 receptor;</li> <li class='image_legend_li'>1 copy of COACTIVATOR PEPTIDE DRIP;</li> <li class='image_legend_li'>1 copy of (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Hetero dimeric assembly 1 of PDB entry 3vt5 coloured by chemically distinct molecules, top view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Vitamin D3 receptor;</li> <li class='image_legend_li'>1 copy of COACTIVATOR PEPTIDE DRIP;</li> <li class='image_legend_li'>1 copy of (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

Assembly 2

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Assembly Name: Vitamin D3 receptor
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Multimeric state: monomeric

Accessible surface area: 11467.87 Å²

Buried surface area: 0.0 Å²

Dissociation area: 0 Å²

Dissociation energy (ΔG^diss): 0 kcal/mol

Dissociation entropy (TΔS^diss): 0 kcal/mol

Symmetry number: 1

PDBe Complex ID: PDB-CPX-146449

$Monomeric assembly 2 of PDB entry 3vt5 coloured by chemically distinct molecules, front view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Vitamin D3 receptor;</li> <li class='image_legend_li'>1 copy of (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Monomeric assembly 2 of PDB entry 3vt5 coloured by chemically distinct molecules, side view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Vitamin D3 receptor;</li> <li class='image_legend_li'>1 copy of (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Monomeric assembly 2 of PDB entry 3vt5 coloured by chemically distinct molecules, top view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>1 copy of Vitamin D3 receptor;</li> <li class='image_legend_li'>1 copy of (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

Macromolecules

Vitamin D3 receptor

Chain: A
Length: 271 amino acids
Theoretical weight: 30.55 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:

Canonical: P13053 (Residues: 116-423; Coverage: 62%)

Gene names: Nr1i1, Vdr
Pfam: Ligand-binding domain of nuclear hormone receptor
InterPro:

Thyroid hormone receptor
Nuclear hormone receptor-like domain superfamily
Nuclear hormone receptor, ligand-binding domain
Nuclear hormone receptor

CATH: Retinoid X Receptor

Vitamin D3 receptor in PDB entry 3vt5, assembly 1, front view.

Vitamin D3 receptor in PDB entry 3vt5, assembly 1, side view.

Vitamin D3 receptor in PDB entry 3vt5, assembly 1, top view.

FASTA Sequence


    >pdb|3vt5|A

GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGSVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLLSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

PDBe-KB: UniProt Coverage View: P13053

Molecule details ›

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FASTA (Protein chains A)
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Structure Factors
SIFTS XML file with residue-level mappings

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BLAST P13053 (UniProt)

COACTIVATOR PEPTIDE DRIP

Chain: C
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Rattus norvegicus
Expression system: Not provided

COACTIVATOR PEPTIDE DRIP in PDB entry 3vt5, assembly 1, side view.

COACTIVATOR PEPTIDE DRIP in PDB entry 3vt5, assembly 1, top view.

FASTA Sequence


    >pdb|3vt5|C

KNHPMLMNLLKDN

Molecule details ›

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FASTA (Protein chains C)
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Updated mmCIF file
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PDBML
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Structure Factors
SIFTS XML file with residue-level mappings

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Similar 3D structures (PDBeFold)
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Protein Data Bank in Europe

Crystal structures of rat VDR-LBD with R270L mutation

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Assemblies

Assembly 1 (preferred)

Assembly 2

Macromolecules

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PDBe › 3vt5 › Structure analysis

Crystal structures of rat VDR-LBD with R270L mutation

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Assemblies

Assembly 1 (preferred)

Assembly 2

Macromolecules

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3vt5 › Structure analysis