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Crystal structures of rat vdr-lbd with R270L mutation

Analyse Crystal structures of rat vdr-lbd with R270L mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VT4
Type: protein
Length: 251 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor; Coactivator peptide drip
UniProt: P13053
Ligands: 5YI
Pockets: 3 · best druggability 0.87

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor	protein	240	64% helix, 3% strand	P13053
C	Coactivator peptide drip	protein	11	64% helix, 0% strand	—

Ligands and binding sites

5YI · (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-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	347	0.87	0.96	44	5YI
2	77	0.35	0.76	17	empty
3	57	0.29	0.74	10	empty

Interfaces

1 interface between chains.

A–C · 566 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3VT4 · Crystal structures of rat VDR-LBD with R270L mutation · 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

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
Elsewhere: RCSB PDB 3VT4 · PDBe 3VT4 · UniProt P13053

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