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Crystal structure of rxralpha ligand-binding domain complexed with corepressor SMRT2 and antagonist rhein

Analyse Crystal structure of rxralpha ligand-binding domain complexed with corepressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3R2A
Type: protein
Length: 866 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor rxr-alpha; Nuclear receptor corepressor 2
UniProt: P19793, Q9Y618
Ligands: RHN
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 65% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinoic acid receptor rxr-alpha	protein	211	65% helix, 3% strand	P19793
B	Retinoic acid receptor rxr-alpha	protein	217	66% helix, 2% strand	P19793
C	Retinoic acid receptor rxr-alpha	protein	203	65% helix, 2% strand	P19793
D	Retinoic acid receptor rxr-alpha	protein	219	65% helix, 3% strand	P19793
E	Nuclear receptor corepressor 2	protein	7	0% helix, 0% strand	Q9Y618
F	Nuclear receptor corepressor 2	protein	9	56% helix, 0% strand	Q9Y618

Ligands and binding sites

RHN · 4,5-dihydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid · ligand · 2 copies · chains A, B, C

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

Pockets

11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	183	0.84	0.98	16	empty
2	818	0.81	0.83	90	RHN
3	538	0.80	0.86	63	empty
4	253	0.80	0.92	35	empty
5	204	0.79	0.94	27	empty

Interfaces

10 interfaces between chains.

B–C · 1410 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 1324 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 1289 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1225 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 530 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3R2A · Crystal structure of RXRalpha ligand-binding domain complexed with corepressor SMRT2 and… · the same entry in another collection · chain D against D, TM-score 1.00
Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain E against A, TM-score 0.63

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 Q9Y618
Elsewhere: RCSB PDB 3R2A · PDBe 3R2A · UniProt P19793 · UniProt Q9Y618

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