MolNFT v1 · #57026 · protein

Crystal structure of the human rxr alpha ligand binding domain bound to a synthetic agonist compound and a coactivator peptide

2ZY0 · Retinoic acid receptor rxr-alpha: “Crystal structure of the human rxr alpha ligand binding domain bound to a synthetic agonist compound and a…”. X-ray diffraction, 1 ligand (21P), 5 pockets (best druggability 0.84). MolNFT v1 #57026…

PDB: 2ZY0
Type: protein
Length: 451 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor rxr-alpha; GRIP1 from nuclear receptor coactivator 2
UniProt: P19793, Q15596
Ligands: 21P
Pockets: 5 · best druggability 0.84

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Retinoic acid receptor rxr-alpha	protein	215	67% helix, 3% strand	P19793
B	GRIP1 from nuclear receptor coactivator 2	protein	10	80% helix, 0% strand	Q15596
D	GRIP1 from nuclear receptor coactivator 2	protein	11	73% helix, 0% strand	Q15596

Ligands and binding sites

21P · 4-[2-(1,1,3,3-tetramethyl-2,3-dihydro-1H-1,3-benzodisilol-5-yl)-1,3-dioxolan-2-yl]benzoic acid · ligand · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.84	0.96	29	21P
2	209	0.83	0.96	28	21P
3	788	0.72	0.78	58	empty
4	91	0.56	0.85	15	empty
5	90	0.55	0.85	17	empty

Interfaces

3 interfaces between chains.

A–C · 1215 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 565 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 562 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2ZY0 · Crystal structure of the human RXR alpha ligand binding domain bound to a synthetic… · the same entry in another collection · chain A against A, TM-score 1.00

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 P19793
Every structure of UniProt Q15596
Elsewhere: RCSB PDB 2ZY0 · PDBe 2ZY0 · UniProt P19793 · UniProt Q15596

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