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Crystal structure of the RARBETA/RXRALPHA ligand binding domain heterodimer in complex with 9-cis retinoic acid and a fragment of the TRAP220 coactivator

Analyse Crystal structure of the RARBETA/RXRALPHA ligand binding domain heterodimer in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XDK
Type: protein
Length: 966 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor rxr-alpha; Retinoic acid receptor, beta; Thyroid receptor…
UniProt: P28700, P22605, Q8BX19
Ligands: 9CR
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 62% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Retinoic acid receptor rxr-alpha	protein	217	63% helix, 3% strand	P28700
B, F	Retinoic acid receptor, beta	protein	245	61% helix, 4% strand	P22605
C, G	Thyroid receptor associated protein 220	protein	11	64% helix, 0% strand	Q8BX19
D, H	Thyroid receptor associated protein 220	protein	10	60% helix, 0% strand	Q8BX19

Ligands and binding sites

9CR · (9cis)-retinoic acid · ligand · 4 copies · chains A, B, E, F

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

Pockets

14 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	332	0.84	0.93	44	9CR
2	325	0.83	0.93	45	9CR
3	218	0.82	0.94	35	9CR
4	218	0.82	0.94	35	9CR
5	575	0.76	0.83	40	empty

Interfaces

9 interfaces between chains.

E–F · 1313 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1311 Å² buried · 17 hydrogen bonds · protein-protein
B–F · 890 Å² buried · 12 hydrogen bonds · protein-protein
E–G · 610 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 608 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1XDK · Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex… · the same entry in another collection · chain H against H, TM-score 1.00
P28700 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- alpha (P28700) · a predicted model of the same protein · chain A against A, TM-score 0.99
P22605 · AlphaFold monomer V2.0 prediction for retinoic acid receptor beta (P22605) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P28700
Every structure of UniProt P22605
Every structure of UniProt Q8BX19
Elsewhere: RCSB PDB 1XDK · PDBe 1XDK · UniProt P28700 · UniProt P22605 · UniProt Q8BX19

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