MolNFT v1 · #129835 · protein

Vitamin D receptor complex

5OW9 · Vitamin D3 receptor a: “Vitamin D receptor complex”. X-ray diffraction, 1 ligand (AYT), 3 pockets (best druggability 0.86). MolNFT v1 #129835 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OW9
Type: protein
Length: 249 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor a; Nuclear receptor coactivator 1
EC: 2.3.1.48
UniProt: Q9PTN2, Q15788
Ligands: AYT
Pockets: 3 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor a	protein	239	66% helix, 3% strand	Q9PTN2
B	Nuclear receptor coactivator 1 (EC 2.3.1.48)	protein	10	60% helix, 0% strand	Q15788

Ligands and binding sites

AYT · (1~{S},3~{Z})-3-[(2~{E})-2-[(1~{S},3~{A}~{S}, 7~{A}~{S})-7~{A}-methyl-1-[(2~{S})-6-methyl-2-oxidanyl-heptan-2-yl]-2,3,3~{A},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	295	0.86	0.96	36	AYT
2	206	0.52	0.77	31	empty
3	61	0.34	0.77	10	empty

Interfaces

1 interface between chains.

A–B · 577 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5OW9 · Vitamin D receptor 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 0.98

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 5OW9 · PDBe 5OW9 · UniProt Q9PTN2 · UniProt Q15788

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