MolNFT v1 · #106278 · protein

Crystal structure of zvdr L337H mutant-vd complex

4RUJ · Vitamin D3 receptor a: “Crystal structure of zvdr L337H mutant-vd complex”. X-ray diffraction, 1 ligand (VDX), 2 pockets (best druggability 0.86). MolNFT v1 #106278 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RUJ
Type: protein
Length: 250 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor a; Nuclear receptor coactivator 1
UniProt: Q9PTN2, Q15788
Ligands: VDX
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor a	protein	240	65% helix, 3% strand	Q9PTN2
B	Nuclear receptor coactivator 1	protein	10	60% helix, 0% strand	Q15788

Ligands and binding sites

VDX · 5-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexane-1,3-diol · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	299	0.86	0.96	37	VDX
2	219	0.51	0.76	28	empty

Interfaces

1 interface between chains.

A–B · 584 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4RUJ · Crystal structure of zVDR L337H mutant-VD complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9PTN2 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor a (Q9PTN2) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9PTN2
Every structure of UniProt Q15788
Elsewhere: RCSB PDB 4RUJ · PDBe 4RUJ · UniProt Q9PTN2 · UniProt Q15788

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