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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

Analyse Crystal structure of the rat vitamin D receptor ligand binding domain complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RJK
Type: protein
Length: 250 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor; Peroxisome proliferator-activated receptor binding protein
UniProt: P13053, Q15648
Ligands: VDZ
Pockets: 3 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor	protein	239	69% helix, 3% strand	P13053
C	Peroxisome proliferator-activated receptor binding protein	protein	11	64% helix, 0% strand	Q15648

Ligands and binding sites

VDZ · 5-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-2-methylene-cyclohexane-1,3-dio L · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	292	0.86	0.96	35	VDZ
2	85	0.35	0.75	17	empty
3	50	0.29	0.76	10	empty

Interfaces

1 interface between chains.

A–C · 543 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1RJK · crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MD… · the same entry in another collection · chain A against A, TM-score 1.00
P13053 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P13053) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.64

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P13053
Every structure of UniProt Q15648
Elsewhere: RCSB PDB 1RJK · PDBe 1RJK · UniProt P13053 · UniProt Q15648

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