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Crystal structure of vdr lbd in complex with 2ALPHA(3-hydroxy-1- propyl) calcitriol

Analyse Crystal structure of vdr lbd in complex with 2ALPHA(3-hydroxy-1- propyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HB7
Type: protein
Length: 254 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor
UniProt: P11473
Ligands: O1C
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 66% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor	protein	254	66% helix, 3% strand	P11473

Ligands and binding sites

O1C · 2alpha-(3-hydroxypropyl)-1alpha,25-dihydroxyvitamin D3 · ligand · chains A

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

Pockets

2 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	320	0.86	0.95	36	O1C
2	64	0.30	0.74	18	empty

Compared structures

2HB7 · Crystal structure of VDR LBD in complex with 2alpha(3-hydroxy-1-propyl) calcitriol · the same entry in another collection · chain A against A, TM-score 1.00
P11473 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P11473) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P11473
Elsewhere: RCSB PDB 2HB7 · PDBe 2HB7 · UniProt P11473

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