MolNFT v1 · #83801 · protein

Crystal structure of vdr-lbd complexed with 22S-butyl-2-methylidene- 19-nor-1A,25-dihydroxyvitamin D3

3WTQ · Vitamin D3 receptor: “Crystal structure of vdr-lbd complexed with 22S-butyl-2-methylidene- 19-nor-1A,25-dihydroxyvitamin D3”. X-ray diffraction, 1 ligand (YS9), 3 pockets (best druggability 0.87). MolNFT v1 #83801 on GenesisL1: 3D…

PDB: 3WTQ
Type: protein
Length: 251 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor; Mediator of RNA polymerase II transcription subunit 1
UniProt: P13053, Q15648
Ligands: YS9
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	protein	240	67% helix, 3% strand	P13053
C	Mediator of RNA polymerase II transcription subunit 1	protein	11	64% helix, 0% strand	Q15648

Ligands and binding sites

YS9 · (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol · 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	352	0.87	0.96	36	YS9
2	112	0.38	0.75	21	empty
3	50	0.29	0.76	10	empty

Interfaces

1 interface between chains.

A–C · 560 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3WTQ · Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxy… · 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 0.65

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 3WTQ · PDBe 3WTQ · UniProt P13053 · UniProt Q15648

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