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crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MD and a synthetic peptide containing the NR2 box of DRIP 205

X-ray diffraction
1.99Å resolution
PDB entry 1rjk coloured by chain, front view.
PDB entry 1rjk coloured by chain, side view.
PDB entry 1rjk coloured by chain, top view.
Source organisms:
Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Mediator of RNA polymerase II transcription subunit 1 and Vitamin D3 receptor
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Multimeric state: hetero dimer
Accessible surface area: 11689.55 Å2
Buried surface area: 2082.65 Å2
Dissociation area: 533.69 Å2
Dissociation energy (ΔGdiss): 4.09 kcal/mol
Dissociation entropy (TΔSdiss): 7.28 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-146463
Assembly 2
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Assembly Name: Mediator of RNA polymerase II transcription subunit 1 and Vitamin D3 receptor
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Multimeric state: hetero tetramer
Accessible surface area: 21821.55 Å2
Buried surface area: 5717.17 Å2
Dissociation area: 787.51 Å2
Dissociation energy (ΔGdiss): 6.33 kcal/mol
Dissociation entropy (TΔSdiss): 12.97 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-146464

Macromolecules

Vitamin D3 receptor
Chain: A
Length: 292 amino acids
Theoretical weight: 32.98 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
SCOP: Nuclear receptor ligand-binding domain
Vitamin D3 receptor in PDB entry 1rjk, assembly 1, front view.
Vitamin D3 receptor in PDB entry 1rjk, assembly 1, side view.
Vitamin D3 receptor in PDB entry 1rjk, assembly 1, 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: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15648 (Residues: 640-652; Coverage: 1%)
Gene names: ARC205, CRSP1, CRSP200, DRIP205, DRIP230, MED1, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2
Mediator of RNA polymerase II transcription subunit 1 in PDB entry 1rjk, assembly 1, front view.
Mediator of RNA polymerase II transcription subunit 1 in PDB entry 1rjk, assembly 1, side view.
Mediator of RNA polymerase II transcription subunit 1 in PDB entry 1rjk, assembly 1, top view.
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