MolNFT v1 · #96933 · protein

Crystal structure of rarbeta lbd in complex with agonist BMS411 [4- {[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl) CARBONYL]AMINO}BENZOIC acid]

4JYG · Retinoic acid receptor beta: “Crystal structure of rarbeta lbd in complex with agonist BMS411 [4…”. X-ray diffraction, 1 ligand (1NY), 8 pockets (best druggability 0.83). MolNFT v1 #96933 on GenesisL1: 3D structure, binding sites…

PDB: 4JYG
Type: protein
Length: 501 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor beta; Steroid receptor coactivator 1
EC: 2.3.1.48
UniProt: P10826, Q15788
Ligands: 1NY
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinoic acid receptor beta	protein	239	68% helix, 4% strand	P10826
B	Retinoic acid receptor beta	protein	240	65% helix, 4% strand	P10826
F, G	Steroid receptor coactivator 1 (EC 2.3.1.48)	protein	11	73% helix, 0% strand	Q15788

Ligands and binding sites

1NY · 4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid · ligand · 2 copies · chains A, B
PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains B
FLC · Citrate anion · additive · chains A, G

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

Pockets

8 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	254	0.83	0.94	38	1NY
2	255	0.83	0.94	37	1NY
3	535	0.71	0.80	51	empty
4	351	0.62	0.78	32	empty
5	113	0.52	0.82	31	empty

Interfaces

3 interfaces between chains.

A–B · 1090 Å² buried · 12 hydrogen bonds · protein-protein
A–G · 533 Å² buried · 4 hydrogen bonds · protein-protein
B–F · 511 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4JYG · Crystal structure of RARbeta LBD in complex with agonist BMS411… · the same entry in another collection · chain A against A, TM-score 1.00
P10826 · AlphaFold monomer V2.0 prediction for retinoic acid receptor beta (P10826) · a predicted model of the same protein · chain B 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 P10826
Every structure of UniProt Q15788
Elsewhere: RCSB PDB 4JYG · PDBe 4JYG · UniProt P10826 · UniProt Q15788

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