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A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket

X-ray diffraction
2.1Å resolution
PDB entry 2zxn coloured by chain, front view.
PDB entry 2zxn coloured by chain, side view.
PDB entry 2zxn coloured by chain, top view.
Source organisms:
Assemblies composition:
monomeric
hetero dimer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: Vitamin D3 receptor
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Multimeric state: monomeric
Accessible surface area: 11475.99 Å2
Buried surface area: 0.0 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-146449
Assembly 2
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Assembly Name: Mediator of RNA polymerase II transcription subunit 1
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Multimeric state: monomeric
Accessible surface area: 1482.83 Å2
Buried surface area: 0.0 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-218856
Assembly 3 (preferred)
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Assembly Name: Vitamin D3 receptor and Mediator of RNA polymerase II transcription subunit 1
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Multimeric state: hetero dimer
Accessible surface area: 11923.48 Å2
Buried surface area: 1035.35 Å2
Dissociation area: 517.67 Å2
Dissociation energy (ΔGdiss): 4.25 kcal/mol
Dissociation entropy (TΔSdiss): 7.54 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-106654

Macromolecules

Vitamin D3 receptor
Chain: A
Length: 271 amino acids
Theoretical weight: 30.6 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:
CATH: Retinoid X Receptor
Vitamin D3 receptor in PDB entry 2zxn, assembly 3, front view.
Vitamin D3 receptor in PDB entry 2zxn, assembly 3, side view.
Vitamin D3 receptor in PDB entry 2zxn, assembly 3, top view.
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Mediator of RNA polymerase II transcription subunit 1
Chain: C
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Xenopus tropicalis
Expression system: Not provided
UniProt:
  • Canonical: A1L0Z0 (Residues: 624-636; Coverage: 1%)
Gene name: med1
Mediator of RNA polymerase II transcription subunit 1 in PDB entry 2zxn, assembly 3, front view.
Mediator of RNA polymerase II transcription subunit 1 in PDB entry 2zxn, assembly 3, side view.
Mediator of RNA polymerase II transcription subunit 1 in PDB entry 2zxn, assembly 3, top view.
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