Research workbench

VDR COMPLEX

Analyse VDR COMPLEX in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OW7
Type: protein
Length: 251 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: AYK
Pockets: 3 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor a	protein	240	67% helix, 3% strand	Q9PTN2
B	Nuclear receptor coactivator 1 (EC 2.3.1.48)	protein	11	64% helix, 0% strand	Q15788

Ligands and binding sites

AYK · (3~{S})-3-[(1~{S},3~{a}~{S},4~{E},7~{a}~{S})-7~{a}-methyl-4-[(2~{Z})-2-[(5~{S})-2-methylidene-5-oxidanyl-cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-3-oxidanyl-~{N}-propan-2-yl-butanamide · 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	305	0.87	0.96	35	AYK
2	201	0.53	0.78	30	empty
3	61	0.33	0.76	10	empty

Interfaces

1 interface between chains.

A–B · 657 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5OW7 · VDR 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 5OW7 · PDBe 5OW7 · UniProt Q9PTN2 · UniProt Q15788

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