Research workbench

Crystal structure at 1.9 angstroems resolution of the homodimer of human rxr alpha ligand binding domain bound to the synthetic agonist compound bms 649 and a coactivator peptide

Analyse Crystal structure at 1.9 angstroems resolution of the homodimer of human rxr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MZN
Type: protein
Length: 916 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rxr retinoid X receptor; Nuclear receptor coactivator 2
UniProt: P19793, Q15596
Ligands: BM6
Pockets: 12 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Rxr retinoid X receptor	protein	224	70% helix, 2% strand	P19793
B, D, F, H	Nuclear receptor coactivator 2	protein	11	73% helix, 0% strand	Q15596
C, G	Rxr retinoid X receptor	protein	212	70% helix, 3% strand	P19793

Ligands and binding sites

BM6 · 4-[2-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-naphthalen-2-yl)-[1,3]dioxolan-2-yl]-benzoic acid · ligand · 4 copies · chains A, C, E, G

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	237	0.84	0.96	33	BM6
2	314	0.84	0.93	41	BM6
3	210	0.84	0.96	27	BM6
4	301	0.83	0.93	41	BM6
5	658	0.69	0.77	55	empty

Interfaces

7 interfaces between chains.

E–G · 1166 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 1150 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 603 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 594 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 576 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1MZN · CRYSTAL STRUCTURE at 1.9 ANGSTROEMS RESOLUTION OF THE HOMODIMER OF HUMAN RXR ALPHA LIGAND… · 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 1MZN · PDBe 1MZN · UniProt P19793 · UniProt Q15596

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.